Starting phenix.real_space_refine on Mon Aug 25 14:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvj_36676/08_2025/8jvj_36676.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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 4824 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: 5 Type Number sf(0) Gaussians S 140 5.16 5 C 16276 2.51 5 N 4204 2.21 5 O 4420 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25052 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4921 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 596} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4921 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 596} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4921 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 596} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4921 Classifications: {'peptide': 620} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 596} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1303 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 170} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "F" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1303 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 170} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "G" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1303 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 170} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "H" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1303 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 170} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'F9M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.21 Number of scatterers: 25052 At special positions: 0 Unit cell: (211.12, 211.12, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 F 12 9.00 O 4420 8.00 N 4204 7.00 C 16276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6056 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 8 sheets defined 63.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.577A pdb=" N ARG A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.801A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 166 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 167 " --> pdb=" O ALA A 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 167' Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.583A pdb=" N ARG A 186 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.528A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.482A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.072A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 260 removed outlier: 4.235A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.837A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.641A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.646A pdb=" N VAL A 365 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.609A pdb=" N GLY A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.514A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.783A pdb=" N LEU A 402 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 403 " --> pdb=" O ARG A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 403' Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 492 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.653A pdb=" N LYS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 569 Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 596 through 611 Processing helix chain 'A' and resid 613 through 636 Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.865A pdb=" N SER A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 691 through 719 removed outlier: 3.526A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 748 removed outlier: 3.734A pdb=" N LYS A 727 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.745A pdb=" N ARG B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.739A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.717A pdb=" N ARG B 186 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.504A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.393A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.843A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.032A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.523A pdb=" N ALA B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.682A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.762A pdb=" N VAL B 365 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.638A pdb=" N GLY B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.635A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.802A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 403 " --> pdb=" O ARG B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 403' Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.730A pdb=" N HIS B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 491 removed outlier: 4.009A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 535 Processing helix chain 'B' and resid 546 through 569 removed outlier: 3.599A pdb=" N ALA B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 589 removed outlier: 4.100A pdb=" N ALA B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.922A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 612 Processing helix chain 'B' and resid 613 through 636 Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.661A pdb=" N SER B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 removed outlier: 3.503A pdb=" N LEU B 686 " --> pdb=" O ASP B 682 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 720 removed outlier: 4.956A pdb=" N LEU B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY B 719 " --> pdb=" O ILE B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 748 removed outlier: 4.493A pdb=" N LYS B 727 " --> pdb=" O GLY B 723 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.531A pdb=" N ARG C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.573A pdb=" N ASP C 165 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.460A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.801A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.847A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.754A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.848A pdb=" N VAL C 365 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.753A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.800A pdb=" N LEU C 402 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.556A pdb=" N ARG C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N HIS C 447 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 4.022A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.790A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 535 Processing helix chain 'C' and resid 546 through 570 Processing helix chain 'C' and resid 573 through 587 removed outlier: 3.687A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 578 " --> pdb=" O TYR C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 596 removed outlier: 3.630A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 611 removed outlier: 3.652A pdb=" N LYS C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 609 " --> pdb=" O MET C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 636 Processing helix chain 'C' and resid 663 through 679 Processing helix chain 'C' and resid 691 through 718 Processing helix chain 'C' and resid 721 through 748 removed outlier: 4.194A pdb=" N LYS C 727 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.840A pdb=" N ASP D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 166 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 167' Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.510A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.462A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 removed outlier: 3.885A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 260 removed outlier: 4.336A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.765A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 357 removed outlier: 3.712A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.639A pdb=" N VAL D 365 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.708A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.825A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 403 " --> pdb=" O ARG D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 399 through 403' Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 442 through 450 removed outlier: 4.608A pdb=" N HIS D 447 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.084A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.620A pdb=" N PHE D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 535 Processing helix chain 'D' and resid 546 through 570 removed outlier: 3.583A pdb=" N ALA D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 removed outlier: 3.741A pdb=" N MET D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 594 removed outlier: 3.621A pdb=" N THR D 593 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 611 removed outlier: 4.381A pdb=" N THR D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 606 " --> pdb=" O TYR D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 635 Processing helix chain 'D' and resid 663 through 679 removed outlier: 3.638A pdb=" N SER D 667 " --> pdb=" O SER D 663 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 719 removed outlier: 3.866A pdb=" N ALA D 716 " --> pdb=" O ASN D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 748 removed outlier: 4.399A pdb=" N LYS D 727 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 729 " --> pdb=" O VAL D 725 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'E' and resid 17 through 28 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.621A pdb=" N GLU E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 124 through 134 removed outlier: 3.768A pdb=" N MET E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 166 through 180 removed outlier: 4.150A pdb=" N GLN E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 27 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.941A pdb=" N GLU F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 94' Processing helix chain 'F' and resid 98 through 107 removed outlier: 3.875A pdb=" N GLU F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.699A pdb=" N ARG F 122 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 119 through 123' Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.821A pdb=" N MET F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.935A pdb=" N GLN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 28 Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 89 through 98 removed outlier: 3.993A pdb=" N GLU G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Proline residue: G 96 - end of helix No H-bonds generated for 'chain 'G' and resid 89 through 98' Processing helix chain 'G' and resid 98 through 107 removed outlier: 3.585A pdb=" N GLU G 102 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.642A pdb=" N ARG G 122 " --> pdb=" O LYS G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.730A pdb=" N MET G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 166 through 180 removed outlier: 4.118A pdb=" N GLN G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 28 Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 89 through 98 removed outlier: 4.329A pdb=" N GLU H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) Proline residue: H 96 - end of helix No H-bonds generated for 'chain 'H' and resid 89 through 98' Processing helix chain 'H' and resid 98 through 107 removed outlier: 3.614A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 123 Processing helix chain 'H' and resid 124 through 134 removed outlier: 3.643A pdb=" N MET H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 166 through 180 removed outlier: 4.068A pdb=" N GLN H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 407 Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 7.137A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 7.191A pdb=" N SER D 416 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.096A pdb=" N TYR E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 80 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 115 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET E 82 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN E 117 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE E 84 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 155 " --> pdb=" O ILE E 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 42 through 47 removed outlier: 4.242A pdb=" N TYR F 42 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE F 4 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS F 6 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TRP F 58 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU F 8 " --> pdb=" O TRP F 58 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL F 79 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS F 7 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU F 81 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL F 9 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS F 83 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL F 11 " --> pdb=" O CYS F 83 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER F 85 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 80 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET F 82 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN F 117 " --> pdb=" O MET F 82 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 84 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N CYS F 159 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY F 116 " --> pdb=" O CYS F 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 47 removed outlier: 4.272A pdb=" N TYR G 42 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE G 4 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA G 56 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS G 6 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TRP G 58 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU G 8 " --> pdb=" O TRP G 58 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL G 79 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS G 7 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU G 81 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL G 9 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS G 83 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL G 11 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N SER G 85 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 80 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL G 115 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET G 82 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN G 117 " --> pdb=" O MET G 82 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE G 84 " --> pdb=" O ASN G 117 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE G 112 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N MET G 157 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU G 114 " --> pdb=" O MET G 157 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS G 159 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLY G 116 " --> pdb=" O CYS G 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 42 through 47 removed outlier: 4.105A pdb=" N TYR H 42 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL H 79 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS H 7 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU H 81 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL H 9 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N CYS H 83 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL H 11 " --> pdb=" O CYS H 83 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N SER H 85 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL H 115 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET H 82 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN H 117 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE H 84 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY H 116 " --> pdb=" O CYS H 159 " (cutoff:3.500A) 1356 hydrogen bonds defined for protein. 3921 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: 4.10 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3936 1.31 - 1.43: 6966 1.43 - 1.56: 14527 1.56 - 1.69: 7 1.69 - 1.82: 212 Bond restraints: 25648 Sorted by residual: bond pdb=" C35 F9M A1201 " pdb=" S02 F9M A1201 " ideal model delta sigma weight residual 1.739 1.497 0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C35 F9M D1201 " pdb=" S02 F9M D1201 " ideal model delta sigma weight residual 1.739 1.507 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C35 F9M B1201 " pdb=" S02 F9M B1201 " ideal model delta sigma weight residual 1.739 1.510 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C35 F9M C1201 " pdb=" S02 F9M C1201 " ideal model delta sigma weight residual 1.739 1.510 0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C34 F9M A1201 " pdb=" S01 F9M A1201 " ideal model delta sigma weight residual 1.727 1.504 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 25643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 34656 3.81 - 7.63: 213 7.63 - 11.44: 11 11.44 - 15.25: 0 15.25 - 19.06: 8 Bond angle restraints: 34888 Sorted by residual: angle pdb=" C32 F9M A1201 " pdb=" S01 F9M A1201 " pdb=" C34 F9M A1201 " ideal model delta sigma weight residual 89.16 108.22 -19.06 3.00e+00 1.11e-01 4.04e+01 angle pdb=" C32 F9M B1201 " pdb=" S01 F9M B1201 " pdb=" C34 F9M B1201 " ideal model delta sigma weight residual 89.16 107.89 -18.73 3.00e+00 1.11e-01 3.90e+01 angle pdb=" C32 F9M C1201 " pdb=" S01 F9M C1201 " pdb=" C34 F9M C1201 " ideal model delta sigma weight residual 89.16 107.65 -18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C32 F9M D1201 " pdb=" S01 F9M D1201 " pdb=" C34 F9M D1201 " ideal model delta sigma weight residual 89.16 107.60 -18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" C35 F9M C1201 " pdb=" S02 F9M C1201 " pdb=" C37 F9M C1201 " ideal model delta sigma weight residual 89.81 107.81 -18.00 3.00e+00 1.11e-01 3.60e+01 ... (remaining 34883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 15019 35.94 - 71.89: 221 71.89 - 107.83: 22 107.83 - 143.77: 6 143.77 - 179.71: 4 Dihedral angle restraints: 15272 sinusoidal: 5888 harmonic: 9384 Sorted by residual: dihedral pdb=" CA LYS A 442 " pdb=" C LYS A 442 " pdb=" N ILE A 443 " pdb=" CA ILE A 443 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" C20 F9M D1201 " pdb=" C22 F9M D1201 " pdb=" N08 F9M D1201 " pdb=" N10 F9M D1201 " ideal model delta sinusoidal sigma weight residual 1.38 -178.33 179.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C20 F9M A1201 " pdb=" C22 F9M A1201 " pdb=" N08 F9M A1201 " pdb=" N10 F9M A1201 " ideal model delta sinusoidal sigma weight residual 1.38 -178.24 179.62 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3533 0.065 - 0.129: 454 0.129 - 0.194: 16 0.194 - 0.259: 7 0.259 - 0.323: 2 Chirality restraints: 4012 Sorted by residual: chirality pdb=" CA ASN A 474 " pdb=" N ASN A 474 " pdb=" C ASN A 474 " pdb=" CB ASN A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN C 474 " pdb=" N ASN C 474 " pdb=" C ASN C 474 " pdb=" CB ASN C 474 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C15 F9M C1201 " pdb=" C17 F9M C1201 " pdb=" C19 F9M C1201 " pdb=" N07 F9M C1201 " both_signs ideal model delta sigma weight residual False -2.86 -2.60 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 4009 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 137 " 0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO F 138 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO F 138 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 138 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 733 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.89e+00 pdb=" CG TRP A 733 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 733 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 733 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 733 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 733 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 733 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 412 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO D 413 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 413 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 413 " -0.042 5.00e-02 4.00e+02 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 280 2.65 - 3.21: 24042 3.21 - 3.77: 39304 3.77 - 4.34: 51169 4.34 - 4.90: 84836 Nonbonded interactions: 199631 Sorted by model distance: nonbonded pdb=" O CYS H 16 " pdb=" ND2 ASN H 117 " model vdw 2.084 3.120 nonbonded pdb=" OH TYR B 691 " pdb=" O GLU C 572 " model vdw 2.091 3.040 nonbonded pdb=" O CYS G 16 " pdb=" ND2 ASN G 117 " model vdw 2.155 3.120 nonbonded pdb=" O LYS A 597 " pdb=" OG1 THR A 601 " model vdw 2.171 3.040 nonbonded pdb=" O GLU A 572 " pdb=" OH TYR D 691 " model vdw 2.203 3.040 ... (remaining 199626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.260 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.010 0.242 25648 Z= 0.487 Angle : 0.751 19.065 34888 Z= 0.363 Chirality : 0.043 0.323 4012 Planarity : 0.004 0.118 4380 Dihedral : 14.735 179.714 9216 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.39 % Allowed : 0.43 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3184 helix: 1.20 (0.12), residues: 1772 sheet: 0.37 (0.36), residues: 260 loop : -0.63 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.036 0.001 TYR A 621 PHE 0.030 0.001 PHE D 617 TRP 0.053 0.002 TRP A 733 HIS 0.002 0.001 HIS D 787 Details of bonding type rmsd covalent geometry : bond 0.00971 (25648) covalent geometry : angle 0.75141 (34888) hydrogen bonds : bond 0.15644 ( 1356) hydrogen bonds : angle 5.70658 ( 3921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 596 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8479 (mmt90) cc_final: 0.8236 (mmt-90) REVERT: A 718 MET cc_start: 0.1400 (tpp) cc_final: -0.0158 (ptt) REVERT: B 442 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7496 (ttpp) REVERT: B 718 MET cc_start: -0.0663 (ppp) cc_final: -0.1207 (ptt) REVERT: C 411 TYR cc_start: 0.5429 (m-10) cc_final: 0.4689 (m-10) REVERT: C 674 PHE cc_start: 0.8300 (m-80) cc_final: 0.8048 (t80) REVERT: E 84 PHE cc_start: 0.7251 (p90) cc_final: 0.6834 (p90) REVERT: F 13 ASP cc_start: 0.5885 (p0) cc_final: 0.5632 (p0) REVERT: F 84 PHE cc_start: 0.7509 (p90) cc_final: 0.6849 (p90) REVERT: F 90 ASP cc_start: 0.8203 (p0) cc_final: 0.7484 (t0) REVERT: G 13 ASP cc_start: 0.6157 (p0) cc_final: 0.5750 (p0) REVERT: H 64 GLU cc_start: 0.7073 (pp20) cc_final: 0.6346 (pm20) REVERT: H 84 PHE cc_start: 0.6979 (p90) cc_final: 0.6751 (p90) outliers start: 10 outliers final: 6 residues processed: 600 average time/residue: 0.1431 time to fit residues: 135.4223 Evaluate side-chains 501 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 495 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 469 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 334 ASN B 338 ASN B 607 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.188697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135969 restraints weight = 43918.077| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.31 r_work: 0.3452 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25648 Z= 0.133 Angle : 0.623 10.102 34888 Z= 0.308 Chirality : 0.041 0.204 4012 Planarity : 0.004 0.072 4380 Dihedral : 9.519 169.529 3660 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.28 % Allowed : 10.00 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 3184 helix: 1.35 (0.12), residues: 1796 sheet: 0.21 (0.36), residues: 260 loop : -0.61 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 237 TYR 0.027 0.001 TYR A 621 PHE 0.023 0.001 PHE B 674 TRP 0.032 0.002 TRP C 733 HIS 0.003 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00290 (25648) covalent geometry : angle 0.62305 (34888) hydrogen bonds : bond 0.04206 ( 1356) hydrogen bonds : angle 4.57187 ( 3921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 528 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8148 (pp20) cc_final: 0.7585 (pp20) REVERT: A 219 ARG cc_start: 0.8971 (mmt90) cc_final: 0.8490 (mmt90) REVERT: A 470 SER cc_start: 0.8398 (m) cc_final: 0.8067 (m) REVERT: A 591 TYR cc_start: 0.6613 (t80) cc_final: 0.6251 (t80) REVERT: B 172 PHE cc_start: 0.8161 (t80) cc_final: 0.7482 (t80) REVERT: B 176 HIS cc_start: 0.8561 (m90) cc_final: 0.8331 (m90) REVERT: B 180 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 219 ARG cc_start: 0.9093 (mmt90) cc_final: 0.8468 (mmp80) REVERT: B 718 MET cc_start: -0.0938 (ppp) cc_final: -0.1256 (ptt) REVERT: C 263 ASP cc_start: 0.8589 (t0) cc_final: 0.8297 (t0) REVERT: C 411 TYR cc_start: 0.6258 (m-10) cc_final: 0.5321 (m-10) REVERT: C 730 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8597 (ptpp) REVERT: C 733 TRP cc_start: 0.8409 (t60) cc_final: 0.8185 (t60) REVERT: D 733 TRP cc_start: 0.8678 (t60) cc_final: 0.8414 (t60) REVERT: E 84 PHE cc_start: 0.7538 (p90) cc_final: 0.6996 (p90) REVERT: E 92 LEU cc_start: 0.7514 (pp) cc_final: 0.7308 (pp) REVERT: E 145 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7535 (mmm160) REVERT: F 84 PHE cc_start: 0.7459 (p90) cc_final: 0.6833 (p90) REVERT: F 145 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7947 (mmm160) REVERT: F 180 GLN cc_start: 0.8456 (pm20) cc_final: 0.8126 (mp10) REVERT: H 13 ASP cc_start: 0.6832 (p0) cc_final: 0.6446 (p0) REVERT: H 64 GLU cc_start: 0.7354 (pp20) cc_final: 0.6697 (pm20) REVERT: H 84 PHE cc_start: 0.7252 (p90) cc_final: 0.6932 (p90) REVERT: H 92 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8381 (pp) outliers start: 33 outliers final: 22 residues processed: 547 average time/residue: 0.1452 time to fit residues: 124.1165 Evaluate side-chains 507 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 483 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 241 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 736 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN D 322 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN H 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.186528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133620 restraints weight = 43682.575| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.25 r_work: 0.3416 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25648 Z= 0.154 Angle : 0.609 10.554 34888 Z= 0.301 Chirality : 0.041 0.188 4012 Planarity : 0.004 0.063 4380 Dihedral : 9.336 178.040 3654 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.09 % Allowed : 13.64 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3184 helix: 1.40 (0.12), residues: 1800 sheet: 0.14 (0.36), residues: 260 loop : -0.63 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 150 TYR 0.022 0.002 TYR A 621 PHE 0.020 0.001 PHE D 341 TRP 0.026 0.002 TRP A 733 HIS 0.005 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00352 (25648) covalent geometry : angle 0.60934 (34888) hydrogen bonds : bond 0.03817 ( 1356) hydrogen bonds : angle 4.34333 ( 3921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 510 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8253 (pp20) cc_final: 0.7700 (pp20) REVERT: A 591 TYR cc_start: 0.6564 (t80) cc_final: 0.6230 (t80) REVERT: B 172 PHE cc_start: 0.8347 (t80) cc_final: 0.7558 (t80) REVERT: B 176 HIS cc_start: 0.8431 (m90) cc_final: 0.8223 (m90) REVERT: B 180 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8663 (tt) REVERT: B 219 ARG cc_start: 0.9129 (mmt90) cc_final: 0.8496 (mmp80) REVERT: B 588 ASN cc_start: 0.7721 (m-40) cc_final: 0.7418 (m-40) REVERT: B 593 THR cc_start: 0.5480 (p) cc_final: 0.5146 (t) REVERT: B 605 MET cc_start: 0.7350 (mtt) cc_final: 0.7027 (mpp) REVERT: B 718 MET cc_start: -0.0614 (ppp) cc_final: -0.0921 (ptt) REVERT: C 219 ARG cc_start: 0.8926 (mmt-90) cc_final: 0.8550 (mmt-90) REVERT: C 263 ASP cc_start: 0.8664 (t0) cc_final: 0.8346 (t0) REVERT: C 411 TYR cc_start: 0.6135 (m-10) cc_final: 0.5195 (m-10) REVERT: D 550 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6801 (mp10) REVERT: D 605 MET cc_start: 0.7968 (mpp) cc_final: 0.7397 (mpp) REVERT: D 733 TRP cc_start: 0.8706 (t60) cc_final: 0.8474 (t60) REVERT: E 84 PHE cc_start: 0.7612 (p90) cc_final: 0.6972 (p90) REVERT: F 84 PHE cc_start: 0.7461 (p90) cc_final: 0.6887 (p90) REVERT: F 93 GLU cc_start: 0.8075 (pm20) cc_final: 0.7822 (pm20) REVERT: F 180 GLN cc_start: 0.8508 (pm20) cc_final: 0.8056 (mp10) REVERT: G 13 ASP cc_start: 0.6126 (p0) cc_final: 0.5386 (p0) REVERT: G 78 ASP cc_start: 0.7795 (m-30) cc_final: 0.7574 (m-30) REVERT: H 13 ASP cc_start: 0.6796 (p0) cc_final: 0.6383 (p0) REVERT: H 64 GLU cc_start: 0.7308 (pp20) cc_final: 0.6664 (pm20) REVERT: H 84 PHE cc_start: 0.7306 (p90) cc_final: 0.6914 (p90) REVERT: H 92 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8370 (pp) REVERT: H 145 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7500 (mmm160) REVERT: H 157 MET cc_start: 0.6360 (ppp) cc_final: 0.6149 (ppp) outliers start: 54 outliers final: 31 residues processed: 543 average time/residue: 0.1386 time to fit residues: 118.8874 Evaluate side-chains 518 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 484 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 96 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134324 restraints weight = 43557.272| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.25 r_work: 0.3439 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25648 Z= 0.121 Angle : 0.593 9.122 34888 Z= 0.291 Chirality : 0.040 0.222 4012 Planarity : 0.004 0.056 4380 Dihedral : 9.169 179.516 3654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.25 % Allowed : 14.84 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3184 helix: 1.47 (0.12), residues: 1804 sheet: 0.09 (0.35), residues: 260 loop : -0.62 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 150 TYR 0.019 0.001 TYR A 621 PHE 0.022 0.001 PHE C 674 TRP 0.026 0.001 TRP A 733 HIS 0.005 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00270 (25648) covalent geometry : angle 0.59319 (34888) hydrogen bonds : bond 0.03548 ( 1356) hydrogen bonds : angle 4.21550 ( 3921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 498 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8201 (pp20) cc_final: 0.7826 (pp20) REVERT: A 449 MET cc_start: 0.8841 (mmm) cc_final: 0.8462 (mtt) REVERT: A 591 TYR cc_start: 0.6770 (t80) cc_final: 0.6467 (t80) REVERT: A 695 PHE cc_start: 0.7706 (m-80) cc_final: 0.6934 (m-80) REVERT: B 172 PHE cc_start: 0.8331 (t80) cc_final: 0.7493 (t80) REVERT: B 219 ARG cc_start: 0.9151 (mmt90) cc_final: 0.8488 (mmp80) REVERT: B 588 ASN cc_start: 0.7746 (m-40) cc_final: 0.7466 (m-40) REVERT: B 591 TYR cc_start: 0.5196 (t80) cc_final: 0.4641 (t80) REVERT: B 718 MET cc_start: -0.0514 (ppp) cc_final: -0.0806 (ptm) REVERT: C 219 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8531 (mmt-90) REVERT: C 263 ASP cc_start: 0.8663 (t0) cc_final: 0.8356 (t0) REVERT: C 411 TYR cc_start: 0.6274 (m-10) cc_final: 0.5249 (m-10) REVERT: D 550 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: D 605 MET cc_start: 0.7881 (mpp) cc_final: 0.7456 (mpp) REVERT: E 84 PHE cc_start: 0.7545 (p90) cc_final: 0.6944 (p90) REVERT: E 145 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7800 (mmm160) REVERT: F 84 PHE cc_start: 0.7292 (p90) cc_final: 0.6771 (p90) REVERT: F 93 GLU cc_start: 0.8046 (pm20) cc_final: 0.7759 (pm20) REVERT: F 145 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7989 (mmm160) REVERT: G 78 ASP cc_start: 0.7785 (m-30) cc_final: 0.7540 (m-30) REVERT: G 164 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6935 (mttm) REVERT: G 180 GLN cc_start: 0.8966 (pt0) cc_final: 0.8165 (tm-30) REVERT: H 13 ASP cc_start: 0.6789 (p0) cc_final: 0.6364 (p0) REVERT: H 64 GLU cc_start: 0.7328 (pp20) cc_final: 0.6669 (pm20) REVERT: H 84 PHE cc_start: 0.7379 (p90) cc_final: 0.6933 (p90) REVERT: H 92 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8472 (pp) REVERT: H 145 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7503 (mmm160) REVERT: H 157 MET cc_start: 0.6447 (ppp) cc_final: 0.6235 (ppp) outliers start: 58 outliers final: 40 residues processed: 534 average time/residue: 0.1314 time to fit residues: 111.0142 Evaluate side-chains 520 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 478 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 221 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 334 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133942 restraints weight = 43493.490| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.36 r_work: 0.3394 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25648 Z= 0.141 Angle : 0.603 10.671 34888 Z= 0.295 Chirality : 0.041 0.224 4012 Planarity : 0.004 0.051 4380 Dihedral : 9.033 179.944 3654 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.67 % Allowed : 16.86 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3184 helix: 1.49 (0.12), residues: 1804 sheet: 0.03 (0.36), residues: 256 loop : -0.66 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 150 TYR 0.016 0.001 TYR A 556 PHE 0.019 0.001 PHE B 172 TRP 0.029 0.002 TRP A 733 HIS 0.007 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00324 (25648) covalent geometry : angle 0.60336 (34888) hydrogen bonds : bond 0.03513 ( 1356) hydrogen bonds : angle 4.17889 ( 3921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8276 (pp20) cc_final: 0.7852 (pp20) REVERT: A 223 MET cc_start: 0.7960 (tmm) cc_final: 0.7754 (tmm) REVERT: A 449 MET cc_start: 0.8864 (mmm) cc_final: 0.8533 (mtt) REVERT: A 591 TYR cc_start: 0.6686 (t80) cc_final: 0.6474 (t80) REVERT: B 591 TYR cc_start: 0.5098 (t80) cc_final: 0.4589 (t80) REVERT: B 593 THR cc_start: 0.5510 (p) cc_final: 0.5213 (t) REVERT: C 219 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8624 (mmt-90) REVERT: C 223 MET cc_start: 0.8120 (tmm) cc_final: 0.7717 (tpp) REVERT: C 263 ASP cc_start: 0.8733 (t0) cc_final: 0.8411 (t0) REVERT: C 411 TYR cc_start: 0.6176 (m-10) cc_final: 0.5127 (m-10) REVERT: D 550 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6848 (mm110) REVERT: D 605 MET cc_start: 0.7852 (mpp) cc_final: 0.7388 (mpp) REVERT: D 736 GLN cc_start: 0.8090 (tt0) cc_final: 0.7841 (tt0) REVERT: E 84 PHE cc_start: 0.7516 (p90) cc_final: 0.6882 (p90) REVERT: E 145 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7691 (mmm160) REVERT: F 84 PHE cc_start: 0.7118 (p90) cc_final: 0.6701 (p90) REVERT: F 93 GLU cc_start: 0.8081 (pm20) cc_final: 0.7744 (pm20) REVERT: F 145 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7948 (mmm160) REVERT: G 78 ASP cc_start: 0.7819 (m-30) cc_final: 0.7561 (m-30) REVERT: G 93 GLU cc_start: 0.8210 (pm20) cc_final: 0.7952 (pm20) REVERT: G 180 GLN cc_start: 0.8900 (pt0) cc_final: 0.8166 (tm-30) REVERT: H 64 GLU cc_start: 0.7361 (pp20) cc_final: 0.6640 (pm20) REVERT: H 84 PHE cc_start: 0.7434 (p90) cc_final: 0.6975 (p90) REVERT: H 92 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8543 (pp) REVERT: H 145 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7567 (mmm160) outliers start: 69 outliers final: 45 residues processed: 538 average time/residue: 0.1409 time to fit residues: 119.1282 Evaluate side-chains 523 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 476 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 319 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 261 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 28 optimal weight: 0.0270 chunk 278 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130284 restraints weight = 43638.693| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.98 r_work: 0.3420 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25648 Z= 0.140 Angle : 0.608 9.378 34888 Z= 0.299 Chirality : 0.041 0.243 4012 Planarity : 0.004 0.055 4380 Dihedral : 8.839 179.963 3654 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.67 % Allowed : 17.64 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3184 helix: 1.50 (0.12), residues: 1804 sheet: 0.00 (0.36), residues: 256 loop : -0.68 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 145 TYR 0.016 0.001 TYR A 556 PHE 0.022 0.001 PHE B 666 TRP 0.034 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00324 (25648) covalent geometry : angle 0.60761 (34888) hydrogen bonds : bond 0.03463 ( 1356) hydrogen bonds : angle 4.13622 ( 3921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 502 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8882 (t80) cc_final: 0.8229 (t80) REVERT: A 218 GLU cc_start: 0.8298 (pp20) cc_final: 0.7886 (pp20) REVERT: A 310 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8020 (tptt) REVERT: A 449 MET cc_start: 0.8812 (mmm) cc_final: 0.8603 (mtt) REVERT: A 591 TYR cc_start: 0.6919 (t80) cc_final: 0.6663 (t80) REVERT: A 748 PHE cc_start: 0.8393 (m-10) cc_final: 0.8161 (m-10) REVERT: B 219 ARG cc_start: 0.9153 (mmt90) cc_final: 0.8428 (mmp80) REVERT: B 578 MET cc_start: 0.7645 (tpp) cc_final: 0.7318 (tpp) REVERT: B 591 TYR cc_start: 0.4490 (t80) cc_final: 0.4036 (t80) REVERT: B 593 THR cc_start: 0.5526 (p) cc_final: 0.5239 (t) REVERT: B 605 MET cc_start: 0.7289 (mtt) cc_final: 0.6992 (mpp) REVERT: C 219 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8607 (mmt-90) REVERT: C 263 ASP cc_start: 0.8673 (t0) cc_final: 0.8347 (t0) REVERT: C 411 TYR cc_start: 0.6271 (m-10) cc_final: 0.5058 (m-10) REVERT: D 550 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6868 (mm110) REVERT: D 736 GLN cc_start: 0.8082 (tt0) cc_final: 0.7762 (tt0) REVERT: E 84 PHE cc_start: 0.7468 (p90) cc_final: 0.6847 (p90) REVERT: E 145 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7617 (mmm160) REVERT: F 84 PHE cc_start: 0.7078 (p90) cc_final: 0.6682 (p90) REVERT: F 93 GLU cc_start: 0.8055 (pm20) cc_final: 0.7618 (pm20) REVERT: F 145 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7926 (mmm160) REVERT: G 78 ASP cc_start: 0.7872 (m-30) cc_final: 0.7439 (m-30) REVERT: G 180 GLN cc_start: 0.8853 (pt0) cc_final: 0.8136 (tm-30) REVERT: H 64 GLU cc_start: 0.7306 (pp20) cc_final: 0.6567 (pm20) REVERT: H 84 PHE cc_start: 0.7415 (p90) cc_final: 0.6950 (p90) REVERT: H 92 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8535 (pp) REVERT: H 145 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7521 (mmm160) outliers start: 69 outliers final: 50 residues processed: 541 average time/residue: 0.1327 time to fit residues: 113.8260 Evaluate side-chains 537 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 574 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 149 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 188 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 235 optimal weight: 0.0060 chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 736 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134502 restraints weight = 43440.083| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.31 r_work: 0.3423 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25648 Z= 0.118 Angle : 0.611 10.990 34888 Z= 0.297 Chirality : 0.041 0.226 4012 Planarity : 0.004 0.048 4380 Dihedral : 8.576 179.111 3654 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.64 % Allowed : 18.76 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 3184 helix: 1.52 (0.12), residues: 1804 sheet: 0.00 (0.35), residues: 256 loop : -0.66 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 145 TYR 0.016 0.001 TYR D 556 PHE 0.023 0.001 PHE B 172 TRP 0.037 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00265 (25648) covalent geometry : angle 0.61076 (34888) hydrogen bonds : bond 0.03349 ( 1356) hydrogen bonds : angle 4.06887 ( 3921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 513 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8287 (pp20) cc_final: 0.7890 (pp20) REVERT: A 223 MET cc_start: 0.8005 (tmm) cc_final: 0.7767 (tmm) REVERT: A 310 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7947 (tptt) REVERT: A 695 PHE cc_start: 0.7641 (m-80) cc_final: 0.6806 (m-80) REVERT: A 748 PHE cc_start: 0.8394 (m-10) cc_final: 0.8140 (m-10) REVERT: B 502 TYR cc_start: 0.7516 (m-80) cc_final: 0.6365 (p90) REVERT: B 578 MET cc_start: 0.7721 (tpp) cc_final: 0.7420 (tpp) REVERT: B 593 THR cc_start: 0.5684 (p) cc_final: 0.5429 (t) REVERT: B 605 MET cc_start: 0.7320 (mtt) cc_final: 0.7086 (mpp) REVERT: C 263 ASP cc_start: 0.8684 (t0) cc_final: 0.8372 (t0) REVERT: C 411 TYR cc_start: 0.6315 (m-10) cc_final: 0.5097 (m-10) REVERT: D 550 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6886 (mm110) REVERT: D 605 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7480 (mpp) REVERT: D 736 GLN cc_start: 0.8081 (tt0) cc_final: 0.7777 (tt0) REVERT: E 84 PHE cc_start: 0.7391 (p90) cc_final: 0.6799 (p90) REVERT: E 145 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7577 (mmm160) REVERT: F 84 PHE cc_start: 0.7069 (p90) cc_final: 0.6728 (p90) REVERT: G 78 ASP cc_start: 0.7804 (m-30) cc_final: 0.7528 (m-30) REVERT: G 93 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8415 (mp0) REVERT: G 180 GLN cc_start: 0.8832 (pt0) cc_final: 0.8133 (tm-30) REVERT: H 64 GLU cc_start: 0.7336 (pp20) cc_final: 0.6396 (pm20) REVERT: H 84 PHE cc_start: 0.7406 (p90) cc_final: 0.6918 (p90) REVERT: H 92 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8512 (pp) REVERT: H 93 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8612 (tm-30) REVERT: H 145 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7528 (mmm160) outliers start: 68 outliers final: 49 residues processed: 550 average time/residue: 0.1395 time to fit residues: 120.8279 Evaluate side-chains 539 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 487 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 72 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130969 restraints weight = 43689.511| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.98 r_work: 0.3432 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25648 Z= 0.132 Angle : 0.636 10.882 34888 Z= 0.308 Chirality : 0.041 0.224 4012 Planarity : 0.004 0.048 4380 Dihedral : 8.412 177.738 3654 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.67 % Allowed : 19.19 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3184 helix: 1.51 (0.12), residues: 1812 sheet: -0.03 (0.35), residues: 256 loop : -0.67 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 145 TYR 0.017 0.001 TYR A 346 PHE 0.021 0.001 PHE B 666 TRP 0.038 0.002 TRP A 733 HIS 0.006 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00301 (25648) covalent geometry : angle 0.63561 (34888) hydrogen bonds : bond 0.03403 ( 1356) hydrogen bonds : angle 4.07760 ( 3921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 492 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8286 (pp20) cc_final: 0.7891 (pp20) REVERT: A 223 MET cc_start: 0.7975 (tmm) cc_final: 0.7751 (tmm) REVERT: A 310 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7917 (tptt) REVERT: A 591 TYR cc_start: 0.6977 (t80) cc_final: 0.6737 (t80) REVERT: A 748 PHE cc_start: 0.8386 (m-10) cc_final: 0.8105 (m-10) REVERT: B 502 TYR cc_start: 0.7465 (m-80) cc_final: 0.6339 (p90) REVERT: B 593 THR cc_start: 0.5681 (p) cc_final: 0.5430 (t) REVERT: B 605 MET cc_start: 0.7364 (mtt) cc_final: 0.7127 (mpp) REVERT: C 263 ASP cc_start: 0.8669 (t0) cc_final: 0.8357 (t0) REVERT: C 411 TYR cc_start: 0.6150 (m-10) cc_final: 0.4922 (m-10) REVERT: D 550 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6893 (mm110) REVERT: D 733 TRP cc_start: 0.8773 (t60) cc_final: 0.8417 (t60) REVERT: D 736 GLN cc_start: 0.8070 (tt0) cc_final: 0.7777 (tt0) REVERT: E 74 TYR cc_start: 0.7721 (m-10) cc_final: 0.7503 (m-10) REVERT: E 84 PHE cc_start: 0.7372 (p90) cc_final: 0.6763 (p90) REVERT: E 145 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7784 (mmm160) REVERT: F 84 PHE cc_start: 0.7030 (p90) cc_final: 0.6716 (p90) REVERT: G 78 ASP cc_start: 0.7846 (m-30) cc_final: 0.7404 (m-30) REVERT: G 180 GLN cc_start: 0.8799 (pt0) cc_final: 0.8125 (tm-30) REVERT: H 64 GLU cc_start: 0.7336 (pp20) cc_final: 0.6384 (pm20) REVERT: H 84 PHE cc_start: 0.7429 (p90) cc_final: 0.6901 (p90) REVERT: H 92 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8288 (pp) REVERT: H 93 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8275 (mp0) REVERT: H 145 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7579 (mmm160) outliers start: 69 outliers final: 56 residues processed: 530 average time/residue: 0.1423 time to fit residues: 119.8403 Evaluate side-chains 542 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 484 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 289 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.0770 chunk 242 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 ASN F 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.186121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133504 restraints weight = 43571.722| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.24 r_work: 0.3403 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25648 Z= 0.149 Angle : 0.650 10.867 34888 Z= 0.316 Chirality : 0.042 0.228 4012 Planarity : 0.004 0.050 4380 Dihedral : 8.322 176.512 3654 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.64 % Allowed : 19.42 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.15), residues: 3184 helix: 1.48 (0.12), residues: 1812 sheet: -0.09 (0.35), residues: 256 loop : -0.70 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 145 TYR 0.017 0.001 TYR A 346 PHE 0.025 0.001 PHE D 172 TRP 0.043 0.002 TRP C 733 HIS 0.006 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00345 (25648) covalent geometry : angle 0.64995 (34888) hydrogen bonds : bond 0.03486 ( 1356) hydrogen bonds : angle 4.10802 ( 3921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 495 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8283 (pp20) cc_final: 0.7870 (pp20) REVERT: A 223 MET cc_start: 0.8026 (tmm) cc_final: 0.7778 (tmm) REVERT: A 310 LYS cc_start: 0.8272 (ttmm) cc_final: 0.8017 (tptt) REVERT: A 748 PHE cc_start: 0.8442 (m-10) cc_final: 0.8185 (m-10) REVERT: B 502 TYR cc_start: 0.7483 (m-80) cc_final: 0.6363 (p90) REVERT: B 593 THR cc_start: 0.5772 (p) cc_final: 0.5508 (t) REVERT: C 263 ASP cc_start: 0.8692 (t0) cc_final: 0.8388 (t0) REVERT: C 379 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8980 (ttmt) REVERT: C 411 TYR cc_start: 0.6157 (m-10) cc_final: 0.4930 (m-10) REVERT: D 550 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6924 (mm110) REVERT: D 733 TRP cc_start: 0.8769 (t60) cc_final: 0.8380 (t60) REVERT: D 736 GLN cc_start: 0.8127 (tt0) cc_final: 0.7835 (tt0) REVERT: E 84 PHE cc_start: 0.7386 (p90) cc_final: 0.6761 (p90) REVERT: E 145 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7844 (mmm160) REVERT: F 24 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7686 (m) REVERT: F 84 PHE cc_start: 0.7027 (p90) cc_final: 0.6723 (p90) REVERT: G 78 ASP cc_start: 0.7840 (m-30) cc_final: 0.7401 (m-30) REVERT: G 157 MET cc_start: 0.7470 (ppp) cc_final: 0.7137 (ppp) REVERT: G 180 GLN cc_start: 0.8823 (pt0) cc_final: 0.8163 (tm-30) REVERT: H 64 GLU cc_start: 0.7315 (pp20) cc_final: 0.6534 (pm20) REVERT: H 84 PHE cc_start: 0.7449 (p90) cc_final: 0.6877 (p90) REVERT: H 145 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7594 (mmm160) outliers start: 68 outliers final: 60 residues processed: 530 average time/residue: 0.1456 time to fit residues: 121.4067 Evaluate side-chains 544 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 481 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 222 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 279 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130624 restraints weight = 43390.949| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.95 r_work: 0.3428 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25648 Z= 0.138 Angle : 0.655 10.783 34888 Z= 0.319 Chirality : 0.042 0.225 4012 Planarity : 0.004 0.057 4380 Dihedral : 8.264 175.986 3654 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.67 % Allowed : 19.50 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.15), residues: 3184 helix: 1.47 (0.12), residues: 1816 sheet: -0.09 (0.35), residues: 256 loop : -0.69 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 145 TYR 0.016 0.001 TYR D 602 PHE 0.018 0.001 PHE B 341 TRP 0.055 0.002 TRP A 733 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00318 (25648) covalent geometry : angle 0.65518 (34888) hydrogen bonds : bond 0.03435 ( 1356) hydrogen bonds : angle 4.09422 ( 3921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6368 Ramachandran restraints generated. 3184 Oldfield, 0 Emsley, 3184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8278 (pp20) cc_final: 0.7865 (pp20) REVERT: A 223 MET cc_start: 0.8006 (tmm) cc_final: 0.7753 (tmm) REVERT: A 310 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7989 (tptt) REVERT: A 591 TYR cc_start: 0.6441 (t80) cc_final: 0.6210 (t80) REVERT: A 748 PHE cc_start: 0.8432 (m-10) cc_final: 0.8138 (m-10) REVERT: B 442 LYS cc_start: 0.7142 (tmmt) cc_final: 0.6941 (pttp) REVERT: B 502 TYR cc_start: 0.7440 (m-80) cc_final: 0.6382 (p90) REVERT: B 593 THR cc_start: 0.5715 (p) cc_final: 0.5460 (t) REVERT: B 605 MET cc_start: 0.7235 (mtt) cc_final: 0.7005 (mpp) REVERT: C 263 ASP cc_start: 0.8685 (t0) cc_final: 0.8382 (t0) REVERT: C 379 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8919 (ttmt) REVERT: C 411 TYR cc_start: 0.6077 (m-10) cc_final: 0.4794 (m-10) REVERT: C 554 PHE cc_start: 0.8557 (t80) cc_final: 0.8305 (t80) REVERT: D 550 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6920 (mm110) REVERT: D 733 TRP cc_start: 0.8761 (t60) cc_final: 0.8358 (t60) REVERT: D 736 GLN cc_start: 0.8088 (tt0) cc_final: 0.7792 (tt0) REVERT: E 84 PHE cc_start: 0.7357 (p90) cc_final: 0.6743 (p90) REVERT: E 145 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7812 (mmm160) REVERT: F 24 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7680 (m) REVERT: F 84 PHE cc_start: 0.7036 (p90) cc_final: 0.6708 (p90) REVERT: G 150 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7745 (ttp-110) REVERT: G 157 MET cc_start: 0.7378 (ppp) cc_final: 0.7065 (ppp) REVERT: G 180 GLN cc_start: 0.8793 (pt0) cc_final: 0.8132 (tm-30) REVERT: H 64 GLU cc_start: 0.7334 (pp20) cc_final: 0.6384 (pm20) REVERT: H 84 PHE cc_start: 0.7484 (p90) cc_final: 0.6841 (p90) REVERT: H 93 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8218 (mp0) REVERT: H 145 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7574 (mmm160) outliers start: 69 outliers final: 62 residues processed: 524 average time/residue: 0.1378 time to fit residues: 114.2180 Evaluate side-chains 542 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 477 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 379 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 695 PHE Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 528 ASN Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 0.0020 chunk 200 optimal weight: 0.9990 chunk 170 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130715 restraints weight = 43330.405| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.96 r_work: 0.3413 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 25648 Z= 0.167 Angle : 0.777 59.197 34888 Z= 0.414 Chirality : 0.042 0.596 4012 Planarity : 0.004 0.065 4380 Dihedral : 8.304 175.975 3654 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.64 % Allowed : 19.50 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.15), residues: 3184 helix: 1.48 (0.12), residues: 1816 sheet: -0.09 (0.35), residues: 256 loop : -0.68 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 145 TYR 0.016 0.001 TYR D 602 PHE 0.018 0.001 PHE B 341 TRP 0.048 0.002 TRP A 733 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00342 (25648) covalent geometry : angle 0.77706 (34888) hydrogen bonds : bond 0.03426 ( 1356) hydrogen bonds : angle 4.09529 ( 3921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6387.02 seconds wall clock time: 109 minutes 44.07 seconds (6584.07 seconds total)