Starting phenix.real_space_refine on Mon May 26 21:36:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvj_36676/05_2025/8jvj_36676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvj_36676/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jvj_36676/05_2025/8jvj_36676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvj_36676/05_2025/8jvj_36676.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvj_36676/05_2025/8jvj_36676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvj_36676/05_2025/8jvj_36676.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 5} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 5} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 5} 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: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, '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: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, '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: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, '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: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 10, '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: 13.93, per 1000 atoms: 0.56 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: 6.67 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.28 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: 8.37 Time building geometry restraints manager: 7.82 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: 0.05 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 53.370 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.180 ------------------------------------------------------------------------------- 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 : 9.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (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 TRP 0.053 0.002 TRP A 733 HIS 0.002 0.001 HIS D 787 PHE 0.030 0.001 PHE D 617 TYR 0.036 0.001 TYR A 621 ARG 0.007 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.15644 ( 1356) hydrogen bonds : angle 5.70658 ( 3921) covalent geometry : bond 0.00971 (25648) covalent geometry : angle 0.75141 (34888) *********************** 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 : 2.578 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: -0.0159 (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: -0.1132 (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: 0.6753 (p90) outliers start: 10 outliers final: 6 residues processed: 600 average time/residue: 0.3514 time to fit residues: 328.7381 Evaluate side-chains 500 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 494 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 270 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 40.0000 chunk 129 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.187199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134422 restraints weight = 43782.256| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.42 r_work: 0.3402 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25648 Z= 0.158 Angle : 0.643 11.440 34888 Z= 0.317 Chirality : 0.041 0.201 4012 Planarity : 0.004 0.074 4380 Dihedral : 9.521 172.519 3660 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.63 % Allowed : 9.92 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3184 helix: 1.27 (0.12), residues: 1800 sheet: 0.17 (0.36), residues: 260 loop : -0.59 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 733 HIS 0.003 0.001 HIS D 176 PHE 0.025 0.002 PHE B 674 TYR 0.027 0.002 TYR A 621 ARG 0.007 0.001 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 1356) hydrogen bonds : angle 4.57042 ( 3921) covalent geometry : bond 0.00358 (25648) covalent geometry : angle 0.64312 (34888) *********************** 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 572 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 530 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8926 (t80) cc_final: 0.8225 (t80) REVERT: A 218 GLU cc_start: 0.8203 (pp20) cc_final: 0.7732 (pp20) REVERT: A 219 ARG cc_start: 0.8993 (mmt90) cc_final: 0.8585 (mmt90) REVERT: A 470 SER cc_start: 0.8408 (m) cc_final: 0.8093 (m) REVERT: A 591 TYR cc_start: 0.6659 (t80) cc_final: 0.6257 (t80) REVERT: A 593 THR cc_start: 0.6975 (p) cc_final: 0.6693 (t) REVERT: B 172 PHE cc_start: 0.8255 (t80) cc_final: 0.7583 (t80) REVERT: B 176 HIS cc_start: 0.8593 (m90) cc_final: 0.8348 (m90) REVERT: B 180 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8739 (tt) REVERT: B 219 ARG cc_start: 0.9110 (mmt90) cc_final: 0.8456 (mmp80) REVERT: B 578 MET cc_start: 0.7829 (tpp) cc_final: 0.7609 (tpp) REVERT: B 718 MET cc_start: -0.0828 (ppp) cc_final: -0.1035 (ptm) REVERT: C 263 ASP cc_start: 0.8662 (t0) cc_final: 0.8356 (t0) REVERT: C 411 TYR cc_start: 0.6157 (m-10) cc_final: 0.5262 (m-10) REVERT: C 482 MET cc_start: 0.6889 (mmm) cc_final: 0.6678 (tpp) REVERT: C 718 MET cc_start: 0.3403 (OUTLIER) cc_final: 0.1741 (mpp) REVERT: C 733 TRP cc_start: 0.8488 (t60) cc_final: 0.8247 (t60) REVERT: D 605 MET cc_start: 0.8116 (mpp) cc_final: 0.7578 (mpp) REVERT: D 733 TRP cc_start: 0.8751 (t60) cc_final: 0.8504 (t60) REVERT: E 84 PHE cc_start: 0.7568 (p90) cc_final: 0.7018 (p90) REVERT: F 84 PHE cc_start: 0.7463 (p90) cc_final: 0.6839 (p90) REVERT: F 145 ARG cc_start: 0.8301 (mmm160) cc_final: 0.8002 (mmm160) REVERT: F 180 GLN cc_start: 0.8444 (pm20) cc_final: 0.8109 (mp10) REVERT: H 13 ASP cc_start: 0.6873 (p0) cc_final: 0.6469 (p0) REVERT: H 37 THR cc_start: 0.7390 (t) cc_final: 0.7189 (m) REVERT: H 41 ASN cc_start: 0.8447 (m-40) cc_final: 0.8243 (m110) REVERT: H 64 GLU cc_start: 0.7370 (pp20) cc_final: 0.6718 (pm20) REVERT: H 84 PHE cc_start: 0.7331 (p90) cc_final: 0.6976 (p90) REVERT: H 92 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8392 (pp) REVERT: H 145 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7456 (mmm160) outliers start: 42 outliers final: 26 residues processed: 556 average time/residue: 0.3534 time to fit residues: 306.7011 Evaluate side-chains 509 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 480 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER 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 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 C residue 718 MET 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 473 ILE Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 THR 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 4 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 287 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 736 GLN B 274 GLN ** B 338 ASN ** 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 440 ASN D 201 ASN D 322 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 736 GLN G 41 ASN H 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131668 restraints weight = 42632.066| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.15 r_work: 0.3357 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 25648 Z= 0.306 Angle : 0.735 10.540 34888 Z= 0.365 Chirality : 0.045 0.224 4012 Planarity : 0.005 0.064 4380 Dihedral : 9.672 179.217 3654 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 14.42 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3184 helix: 1.03 (0.12), residues: 1800 sheet: -0.08 (0.35), residues: 260 loop : -0.76 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 733 HIS 0.008 0.001 HIS C 176 PHE 0.025 0.002 PHE C 471 TYR 0.021 0.002 TYR C 235 ARG 0.007 0.001 ARG B 779 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 1356) hydrogen bonds : angle 4.60634 ( 3921) covalent geometry : bond 0.00708 (25648) covalent geometry : angle 0.73549 (34888) *********************** 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 574 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 497 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.8819 (mmm) cc_final: 0.8386 (mtt) REVERT: B 172 PHE cc_start: 0.8213 (t80) cc_final: 0.7426 (t80) REVERT: B 180 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 219 ARG cc_start: 0.9025 (mmt90) cc_final: 0.8460 (mmp80) REVERT: B 593 THR cc_start: 0.6160 (p) cc_final: 0.5815 (t) REVERT: C 219 ARG cc_start: 0.8813 (mmt90) cc_final: 0.8580 (mmt-90) REVERT: C 411 TYR cc_start: 0.6019 (m-10) cc_final: 0.5199 (m-10) REVERT: D 550 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7033 (mm110) REVERT: D 605 MET cc_start: 0.8257 (mpp) cc_final: 0.7574 (mpp) REVERT: D 733 TRP cc_start: 0.8780 (t60) cc_final: 0.8559 (t60) REVERT: E 84 PHE cc_start: 0.7566 (p90) cc_final: 0.7029 (p90) REVERT: E 145 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7765 (mmm160) REVERT: F 59 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7782 (p0) REVERT: F 78 ASP cc_start: 0.7941 (m-30) cc_final: 0.7741 (m-30) REVERT: F 84 PHE cc_start: 0.7446 (p90) cc_final: 0.6846 (p90) REVERT: F 93 GLU cc_start: 0.8251 (pm20) cc_final: 0.8017 (pm20) REVERT: G 13 ASP cc_start: 0.6204 (p0) cc_final: 0.5815 (p0) REVERT: H 13 ASP cc_start: 0.6762 (p0) cc_final: 0.6312 (p0) REVERT: H 84 PHE cc_start: 0.7296 (p90) cc_final: 0.6990 (p90) REVERT: H 92 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8469 (pp) REVERT: H 94 ASN cc_start: 0.8201 (t0) cc_final: 0.7727 (t0) REVERT: H 145 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7465 (mmm160) outliers start: 77 outliers final: 45 residues processed: 546 average time/residue: 0.3565 time to fit residues: 303.7730 Evaluate side-chains 530 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 481 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 517 THR 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 250 CYS Chi-restraints excluded: chain B residue 309 HIS 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 B residue 556 TYR Chi-restraints excluded: chain B residue 732 ILE 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 440 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 574 TYR 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 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 THR 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 59 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 Chi-restraints excluded: chain H residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 246 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 306 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 216 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** 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 440 ASN ** D 338 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 = 0.4271 r_free = 0.4271 target = 0.185744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133014 restraints weight = 43508.744| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.16 r_work: 0.3394 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25648 Z= 0.123 Angle : 0.607 10.617 34888 Z= 0.302 Chirality : 0.041 0.202 4012 Planarity : 0.004 0.057 4380 Dihedral : 9.311 179.058 3654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.36 % Allowed : 16.24 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3184 helix: 1.26 (0.12), residues: 1800 sheet: -0.08 (0.35), residues: 260 loop : -0.70 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 733 HIS 0.010 0.001 HIS B 176 PHE 0.023 0.001 PHE B 172 TYR 0.020 0.001 TYR D 556 ARG 0.008 0.000 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1356) hydrogen bonds : angle 4.29764 ( 3921) covalent geometry : bond 0.00262 (25648) covalent geometry : angle 0.60689 (34888) *********************** 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 576 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 515 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8267 (ttmm) cc_final: 0.8040 (tptt) REVERT: A 449 MET cc_start: 0.8778 (mmm) cc_final: 0.8415 (mtt) REVERT: A 605 MET cc_start: 0.7496 (mtp) cc_final: 0.7263 (mpp) REVERT: B 219 ARG cc_start: 0.9178 (mmt90) cc_final: 0.8479 (mmp80) REVERT: B 593 THR cc_start: 0.5545 (p) cc_final: 0.5237 (t) REVERT: C 263 ASP cc_start: 0.8719 (t0) cc_final: 0.8391 (t0) REVERT: C 411 TYR cc_start: 0.6342 (m-10) cc_final: 0.5156 (m-10) REVERT: C 733 TRP cc_start: 0.8550 (t60) cc_final: 0.8294 (t60) REVERT: D 550 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6846 (mm110) REVERT: D 605 MET cc_start: 0.8278 (mpp) cc_final: 0.7723 (mpp) REVERT: E 84 PHE cc_start: 0.7623 (p90) cc_final: 0.7021 (p90) REVERT: E 145 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7671 (mmm160) REVERT: F 65 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6533 (t0) REVERT: F 68 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7469 (ptt-90) REVERT: F 78 ASP cc_start: 0.7974 (m-30) cc_final: 0.7709 (m-30) REVERT: F 84 PHE cc_start: 0.7298 (p90) cc_final: 0.6772 (p90) REVERT: F 93 GLU cc_start: 0.8060 (pm20) cc_final: 0.7780 (pm20) REVERT: F 145 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7967 (mmm160) REVERT: F 180 GLN cc_start: 0.8883 (pt0) cc_final: 0.8236 (tp-100) REVERT: G 78 ASP cc_start: 0.7699 (m-30) cc_final: 0.7465 (m-30) REVERT: G 97 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: G 180 GLN cc_start: 0.8202 (pm20) cc_final: 0.7991 (tm-30) REVERT: H 64 GLU cc_start: 0.7345 (pp20) cc_final: 0.6274 (pm20) REVERT: H 84 PHE cc_start: 0.7463 (p90) cc_final: 0.6991 (p90) REVERT: H 92 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8525 (pp) REVERT: H 145 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7506 (mmm160) outliers start: 61 outliers final: 40 residues processed: 547 average time/residue: 0.3657 time to fit residues: 313.0031 Evaluate side-chains 524 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 480 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU 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 611 PHE Chi-restraints excluded: chain A residue 632 LEU 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 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 440 ASN 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 718 MET Chi-restraints excluded: chain C residue 762 VAL 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 473 ILE Chi-restraints excluded: chain D residue 479 LEU 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 750 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 48 VAL Chi-restraints excluded: chain F residue 65 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 G residue 45 ASP Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 45 ASP 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 125 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 276 optimal weight: 0.0050 chunk 157 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.1800 ------------------------------------------------------------------------------- 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 338 ASN ** 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.181954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127200 restraints weight = 43436.428| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.13 r_work: 0.3341 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25648 Z= 0.225 Angle : 0.665 10.560 34888 Z= 0.329 Chirality : 0.043 0.188 4012 Planarity : 0.004 0.052 4380 Dihedral : 9.266 178.862 3654 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.29 % Allowed : 17.79 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3184 helix: 1.19 (0.12), residues: 1800 sheet: -0.19 (0.35), residues: 260 loop : -0.79 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 733 HIS 0.008 0.001 HIS D 176 PHE 0.021 0.002 PHE D 341 TYR 0.018 0.002 TYR C 491 ARG 0.010 0.001 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1356) hydrogen bonds : angle 4.37780 ( 3921) covalent geometry : bond 0.00525 (25648) covalent geometry : angle 0.66523 (34888) *********************** 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 578 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 493 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8815 (pt0) cc_final: 0.8049 (pp20) REVERT: A 449 MET cc_start: 0.8855 (mmm) cc_final: 0.8484 (mtt) REVERT: A 591 TYR cc_start: 0.6964 (t80) cc_final: 0.6723 (t80) REVERT: B 219 ARG cc_start: 0.9212 (mmt90) cc_final: 0.8493 (mmp80) REVERT: B 223 MET cc_start: 0.8224 (tpp) cc_final: 0.8009 (tpp) REVERT: B 350 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8487 (tp) REVERT: B 588 ASN cc_start: 0.7975 (m-40) cc_final: 0.7605 (m-40) REVERT: B 593 THR cc_start: 0.5878 (p) cc_final: 0.5543 (t) REVERT: C 411 TYR cc_start: 0.6193 (m-10) cc_final: 0.5041 (m-10) REVERT: D 605 MET cc_start: 0.8256 (mpp) cc_final: 0.7717 (mpp) REVERT: D 733 TRP cc_start: 0.8808 (t60) cc_final: 0.8574 (t60) REVERT: D 736 GLN cc_start: 0.8148 (tt0) cc_final: 0.7792 (tt0) REVERT: E 84 PHE cc_start: 0.7596 (p90) cc_final: 0.6983 (p90) REVERT: E 145 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7566 (mmm160) REVERT: F 78 ASP cc_start: 0.8028 (m-30) cc_final: 0.7762 (m-30) REVERT: F 84 PHE cc_start: 0.7231 (p90) cc_final: 0.6792 (p90) REVERT: F 93 GLU cc_start: 0.8095 (pm20) cc_final: 0.7784 (pm20) REVERT: F 145 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7984 (mmm160) REVERT: H 64 GLU cc_start: 0.7144 (pp20) cc_final: 0.6028 (pm20) REVERT: H 84 PHE cc_start: 0.7561 (p90) cc_final: 0.7027 (p90) REVERT: H 92 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8552 (pp) REVERT: H 145 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7529 (mmm160) REVERT: H 157 MET cc_start: 0.8220 (ptp) cc_final: 0.7732 (ppp) outliers start: 85 outliers final: 59 residues processed: 548 average time/residue: 0.3505 time to fit residues: 301.7112 Evaluate side-chains 533 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 472 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 ASN 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 598 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain B residue 163 THR 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 350 LEU 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 325 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 440 ASN 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 562 VAL Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR 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 227 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 349 LEU 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 550 GLN Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 750 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 48 VAL Chi-restraints excluded: chain F residue 48 VAL 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 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 191 optimal weight: 0.6980 chunk 237 optimal weight: 20.0000 chunk 267 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 338 ASN ** 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 440 ASN G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.184910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132199 restraints weight = 43190.176| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.39 r_work: 0.3370 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25648 Z= 0.126 Angle : 0.615 11.086 34888 Z= 0.302 Chirality : 0.041 0.174 4012 Planarity : 0.004 0.050 4380 Dihedral : 9.018 178.713 3654 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.83 % Allowed : 19.26 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3184 helix: 1.31 (0.12), residues: 1800 sheet: -0.23 (0.35), residues: 260 loop : -0.76 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 PHE 0.020 0.001 PHE D 341 TYR 0.019 0.001 TYR D 556 ARG 0.010 0.000 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1356) hydrogen bonds : angle 4.23028 ( 3921) covalent geometry : bond 0.00284 (25648) covalent geometry : angle 0.61514 (34888) *********************** 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 576 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 503 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8029 (tmm) cc_final: 0.7762 (tmm) REVERT: A 310 LYS cc_start: 0.8279 (ttmm) cc_final: 0.8018 (tptt) REVERT: A 449 MET cc_start: 0.8745 (mmm) cc_final: 0.8541 (mtt) REVERT: B 219 ARG cc_start: 0.9224 (mmt90) cc_final: 0.8491 (mmp80) REVERT: B 502 TYR cc_start: 0.7623 (m-80) cc_final: 0.6458 (p90) REVERT: B 591 TYR cc_start: 0.4707 (t80) cc_final: 0.4137 (t80) REVERT: B 593 THR cc_start: 0.5597 (p) cc_final: 0.5301 (t) REVERT: C 263 ASP cc_start: 0.8770 (t0) cc_final: 0.8449 (t0) REVERT: C 411 TYR cc_start: 0.6200 (m-10) cc_final: 0.4960 (m-10) REVERT: C 733 TRP cc_start: 0.8549 (t60) cc_final: 0.8344 (t60) REVERT: D 550 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6883 (mm110) REVERT: D 605 MET cc_start: 0.8227 (mpp) cc_final: 0.7701 (mpp) REVERT: E 84 PHE cc_start: 0.7444 (p90) cc_final: 0.6848 (p90) REVERT: E 145 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7617 (mmm160) REVERT: F 24 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7607 (m) REVERT: F 78 ASP cc_start: 0.8042 (m-30) cc_final: 0.7760 (m-30) REVERT: F 84 PHE cc_start: 0.7062 (p90) cc_final: 0.6640 (p90) REVERT: F 93 GLU cc_start: 0.8127 (pm20) cc_final: 0.7791 (pm20) REVERT: F 180 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8223 (tp-100) REVERT: H 64 GLU cc_start: 0.7363 (pp20) cc_final: 0.6284 (pm20) REVERT: H 84 PHE cc_start: 0.7561 (p90) cc_final: 0.7002 (p90) REVERT: H 92 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8544 (pp) REVERT: H 145 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7532 (mmm160) REVERT: H 157 MET cc_start: 0.8243 (ptp) cc_final: 0.7736 (ppp) outliers start: 73 outliers final: 49 residues processed: 548 average time/residue: 0.3520 time to fit residues: 302.6520 Evaluate side-chains 540 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 487 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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 587 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 682 ASP 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 C residue 319 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU 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 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 319 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 469 VAL 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 33 VAL Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 164 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 304 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 338 ASN ** 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 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 = 0.4288 r_free = 0.4288 target = 0.187133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134242 restraints weight = 42545.297| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.00 r_work: 0.3400 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25648 Z= 0.203 Angle : 0.668 10.967 34888 Z= 0.327 Chirality : 0.042 0.173 4012 Planarity : 0.004 0.050 4380 Dihedral : 8.960 177.222 3654 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.57 % Allowed : 19.30 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3184 helix: 1.27 (0.12), residues: 1804 sheet: -0.27 (0.34), residues: 260 loop : -0.79 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 733 HIS 0.006 0.001 HIS D 252 PHE 0.021 0.002 PHE D 341 TYR 0.017 0.002 TYR D 556 ARG 0.011 0.001 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 1356) hydrogen bonds : angle 4.29805 ( 3921) covalent geometry : bond 0.00471 (25648) covalent geometry : angle 0.66768 (34888) *********************** 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 576 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 484 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8345 (tmm) cc_final: 0.8081 (tmm) REVERT: A 591 TYR cc_start: 0.7387 (t80) cc_final: 0.7158 (t80) REVERT: B 219 ARG cc_start: 0.9073 (mmt90) cc_final: 0.8448 (mmp80) REVERT: B 350 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 588 ASN cc_start: 0.7987 (m-40) cc_final: 0.7602 (m-40) REVERT: B 591 TYR cc_start: 0.5418 (t80) cc_final: 0.4800 (t80) REVERT: B 593 THR cc_start: 0.5966 (p) cc_final: 0.5693 (t) REVERT: C 223 MET cc_start: 0.8492 (tmm) cc_final: 0.8050 (tpp) REVERT: C 411 TYR cc_start: 0.5916 (m-10) cc_final: 0.4839 (m-10) REVERT: C 733 TRP cc_start: 0.8475 (t60) cc_final: 0.8261 (t60) REVERT: D 219 ARG cc_start: 0.8910 (mmt90) cc_final: 0.8256 (mmp80) REVERT: D 605 MET cc_start: 0.8309 (mpp) cc_final: 0.7776 (mpp) REVERT: D 733 TRP cc_start: 0.8795 (t60) cc_final: 0.8588 (t60) REVERT: E 84 PHE cc_start: 0.7319 (p90) cc_final: 0.6764 (p90) REVERT: E 145 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7737 (mmm160) REVERT: F 24 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7778 (m) REVERT: F 78 ASP cc_start: 0.7956 (m-30) cc_final: 0.7742 (m-30) REVERT: F 84 PHE cc_start: 0.7044 (p90) cc_final: 0.6618 (p90) REVERT: F 93 GLU cc_start: 0.8163 (pm20) cc_final: 0.7902 (pm20) REVERT: G 24 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7283 (m) REVERT: H 64 GLU cc_start: 0.7052 (pp20) cc_final: 0.6132 (pm20) REVERT: H 84 PHE cc_start: 0.7442 (p90) cc_final: 0.6971 (p90) REVERT: H 92 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8546 (pp) REVERT: H 145 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7522 (mmm160) REVERT: H 157 MET cc_start: 0.7975 (ptp) cc_final: 0.7640 (ppp) outliers start: 92 outliers final: 69 residues processed: 542 average time/residue: 0.3709 time to fit residues: 316.8005 Evaluate side-chains 544 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 471 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 349 LEU 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 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 682 ASP 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 349 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 440 ASN 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 559 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 TYR 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 349 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 750 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 48 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 164 LYS 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 150 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 317 optimal weight: 0.0020 chunk 69 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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 338 ASN ** 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 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 = 0.4323 r_free = 0.4323 target = 0.190451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136946 restraints weight = 42492.507| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.18 r_work: 0.3439 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25648 Z= 0.120 Angle : 0.629 11.487 34888 Z= 0.307 Chirality : 0.041 0.183 4012 Planarity : 0.004 0.048 4380 Dihedral : 8.638 176.538 3654 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.83 % Allowed : 20.12 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3184 helix: 1.34 (0.12), residues: 1812 sheet: -0.26 (0.35), residues: 256 loop : -0.76 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 733 HIS 0.006 0.001 HIS D 252 PHE 0.020 0.001 PHE D 341 TYR 0.019 0.001 TYR D 556 ARG 0.011 0.000 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 1356) hydrogen bonds : angle 4.18255 ( 3921) covalent geometry : bond 0.00271 (25648) covalent geometry : angle 0.62870 (34888) *********************** 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 565 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 492 time to evaluate : 2.717 Fit side-chains REVERT: A 223 MET cc_start: 0.8380 (tmm) cc_final: 0.8078 (tmm) REVERT: B 219 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8455 (mmp80) REVERT: B 350 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 502 TYR cc_start: 0.7359 (m-80) cc_final: 0.6393 (p90) REVERT: B 593 THR cc_start: 0.5983 (p) cc_final: 0.5749 (t) REVERT: B 605 MET cc_start: 0.7498 (mtt) cc_final: 0.7292 (mpp) REVERT: B 718 MET cc_start: -0.1004 (ptt) cc_final: -0.3513 (mtm) REVERT: C 223 MET cc_start: 0.8508 (tmm) cc_final: 0.8098 (tpp) REVERT: C 263 ASP cc_start: 0.8612 (t0) cc_final: 0.8364 (t0) REVERT: C 411 TYR cc_start: 0.5818 (m-10) cc_final: 0.4686 (m-10) REVERT: C 578 MET cc_start: 0.7726 (tpp) cc_final: 0.7449 (ttp) REVERT: C 733 TRP cc_start: 0.8459 (t60) cc_final: 0.8251 (t60) REVERT: D 219 ARG cc_start: 0.9027 (mmt90) cc_final: 0.8236 (mmp80) REVERT: D 550 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7109 (mm110) REVERT: D 553 TYR cc_start: 0.8637 (m-80) cc_final: 0.8220 (m-80) REVERT: D 605 MET cc_start: 0.8350 (mpp) cc_final: 0.7878 (mpp) REVERT: D 713 MET cc_start: 0.8419 (tmm) cc_final: 0.7305 (mtp) REVERT: E 84 PHE cc_start: 0.7309 (p90) cc_final: 0.6703 (p90) REVERT: E 145 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7817 (mmm160) REVERT: F 24 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7723 (m) REVERT: F 84 PHE cc_start: 0.7051 (p90) cc_final: 0.6668 (p90) REVERT: F 93 GLU cc_start: 0.8153 (pm20) cc_final: 0.7888 (pm20) REVERT: F 95 ILE cc_start: 0.8110 (mm) cc_final: 0.7906 (mm) REVERT: G 157 MET cc_start: 0.7311 (ppp) cc_final: 0.6848 (ppp) REVERT: G 180 GLN cc_start: 0.9125 (pt0) cc_final: 0.8244 (tm-30) REVERT: H 64 GLU cc_start: 0.7289 (pp20) cc_final: 0.6320 (pm20) REVERT: H 84 PHE cc_start: 0.7439 (p90) cc_final: 0.6915 (p90) REVERT: H 92 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8504 (pp) REVERT: H 93 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8478 (tm-30) REVERT: H 145 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7470 (mmm160) REVERT: H 157 MET cc_start: 0.7923 (ptp) cc_final: 0.7624 (ppp) outliers start: 73 outliers final: 53 residues processed: 538 average time/residue: 0.3555 time to fit residues: 299.2636 Evaluate side-chains 534 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 477 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE 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 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 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 762 VAL Chi-restraints excluded: chain D residue 195 LEU 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 342 VAL Chi-restraints excluded: chain D residue 450 LEU 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 550 GLN Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 618 LEU 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 48 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 90 ASP 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 G residue 164 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 180 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 318 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 223 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 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** G 41 ASN 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 = 0.186465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133975 restraints weight = 43702.647| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.43 r_work: 0.3388 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25648 Z= 0.116 Angle : 0.644 11.289 34888 Z= 0.311 Chirality : 0.041 0.200 4012 Planarity : 0.004 0.080 4380 Dihedral : 8.364 174.837 3654 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.48 % Allowed : 21.05 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3184 helix: 1.41 (0.12), residues: 1808 sheet: -0.22 (0.35), residues: 256 loop : -0.78 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 PHE 0.033 0.001 PHE C 172 TYR 0.022 0.001 TYR D 602 ARG 0.012 0.000 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 1356) hydrogen bonds : angle 4.15100 ( 3921) covalent geometry : bond 0.00257 (25648) covalent geometry : angle 0.64424 (34888) *********************** 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 562 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 498 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8097 (tmm) cc_final: 0.7789 (tmm) REVERT: A 591 TYR cc_start: 0.6942 (t80) cc_final: 0.6457 (t80) REVERT: B 502 TYR cc_start: 0.7532 (m-80) cc_final: 0.6520 (p90) REVERT: B 588 ASN cc_start: 0.7816 (m-40) cc_final: 0.7469 (m-40) REVERT: B 593 THR cc_start: 0.5713 (p) cc_final: 0.5488 (t) REVERT: B 718 MET cc_start: -0.0956 (ptt) cc_final: -0.3468 (mtm) REVERT: C 223 MET cc_start: 0.8311 (tmm) cc_final: 0.7880 (tpp) REVERT: C 411 TYR cc_start: 0.5978 (m-10) cc_final: 0.4863 (m-80) REVERT: C 554 PHE cc_start: 0.8798 (t80) cc_final: 0.8479 (m-80) REVERT: C 605 MET cc_start: 0.5924 (ptm) cc_final: 0.4545 (mmp) REVERT: C 733 TRP cc_start: 0.8492 (t60) cc_final: 0.8234 (t60) REVERT: D 550 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6908 (mm110) REVERT: D 553 TYR cc_start: 0.8520 (m-80) cc_final: 0.8237 (m-80) REVERT: D 605 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7790 (mpp) REVERT: D 733 TRP cc_start: 0.8778 (t60) cc_final: 0.8452 (t60) REVERT: E 84 PHE cc_start: 0.7396 (p90) cc_final: 0.6758 (p90) REVERT: E 145 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7797 (mmm160) REVERT: F 24 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7551 (m) REVERT: F 84 PHE cc_start: 0.7025 (p90) cc_final: 0.6697 (p90) REVERT: G 157 MET cc_start: 0.7283 (ppp) cc_final: 0.6956 (ppp) REVERT: G 180 GLN cc_start: 0.9026 (pt0) cc_final: 0.8256 (tm-30) REVERT: H 64 GLU cc_start: 0.7479 (pp20) cc_final: 0.6502 (pm20) REVERT: H 84 PHE cc_start: 0.7580 (p90) cc_final: 0.6996 (p90) REVERT: H 92 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8717 (pp) REVERT: H 145 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7660 (mmm160) REVERT: H 157 MET cc_start: 0.8258 (ptp) cc_final: 0.7750 (ppp) outliers start: 64 outliers final: 48 residues processed: 540 average time/residue: 0.3656 time to fit residues: 309.8339 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 : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE 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 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 469 VAL 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 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU 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 342 VAL 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 550 GLN Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 750 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 48 VAL Chi-restraints excluded: chain F residue 65 ASP 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 G residue 159 CYS Chi-restraints excluded: chain G residue 164 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 180 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 88 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 261 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 338 ASN ** 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 607 GLN C 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.186526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130748 restraints weight = 43447.472| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.98 r_work: 0.3425 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25648 Z= 0.123 Angle : 0.665 10.985 34888 Z= 0.320 Chirality : 0.042 0.210 4012 Planarity : 0.004 0.059 4380 Dihedral : 8.206 173.779 3654 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.17 % Allowed : 21.55 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3184 helix: 1.39 (0.12), residues: 1812 sheet: -0.18 (0.35), residues: 256 loop : -0.73 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 PHE 0.029 0.001 PHE C 172 TYR 0.033 0.001 TYR D 602 ARG 0.013 0.000 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 1356) hydrogen bonds : angle 4.14772 ( 3921) covalent geometry : bond 0.00280 (25648) covalent geometry : angle 0.66495 (34888) ********************** 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 540 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 484 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.8086 (m-80) cc_final: 0.7848 (m-80) REVERT: B 502 TYR cc_start: 0.7444 (m-80) cc_final: 0.6443 (p90) REVERT: B 588 ASN cc_start: 0.7728 (m-40) cc_final: 0.7352 (m-40) REVERT: B 593 THR cc_start: 0.5685 (p) cc_final: 0.5394 (t) REVERT: B 605 MET cc_start: 0.7487 (mpp) cc_final: 0.6917 (mpp) REVERT: B 718 MET cc_start: -0.1103 (ptt) cc_final: -0.3564 (mtm) REVERT: C 223 MET cc_start: 0.8281 (tmm) cc_final: 0.7896 (tpp) REVERT: C 411 TYR cc_start: 0.5892 (m-10) cc_final: 0.4732 (m-80) REVERT: C 554 PHE cc_start: 0.8797 (t80) cc_final: 0.8350 (m-80) REVERT: C 605 MET cc_start: 0.5789 (ptm) cc_final: 0.4396 (mmp) REVERT: C 733 TRP cc_start: 0.8495 (t60) cc_final: 0.8231 (t60) REVERT: D 550 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6887 (mm110) REVERT: D 553 TYR cc_start: 0.8443 (m-80) cc_final: 0.8221 (m-80) REVERT: D 605 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7764 (mpp) REVERT: D 733 TRP cc_start: 0.8734 (t60) cc_final: 0.8383 (t60) REVERT: D 736 GLN cc_start: 0.8030 (tt0) cc_final: 0.7752 (tt0) REVERT: E 84 PHE cc_start: 0.7344 (p90) cc_final: 0.6725 (p90) REVERT: F 24 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7679 (m) REVERT: F 84 PHE cc_start: 0.6988 (p90) cc_final: 0.6689 (p90) REVERT: F 98 LYS cc_start: 0.6054 (tmmt) cc_final: 0.5828 (tmmt) REVERT: G 8 LEU cc_start: 0.8121 (tp) cc_final: 0.7837 (tp) REVERT: G 150 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7769 (ttp-110) REVERT: G 157 MET cc_start: 0.7220 (ppp) cc_final: 0.6871 (ppp) REVERT: G 180 GLN cc_start: 0.8968 (pt0) cc_final: 0.8243 (tm-30) REVERT: H 64 GLU cc_start: 0.7382 (pp20) cc_final: 0.6420 (pm20) REVERT: H 84 PHE cc_start: 0.7576 (p90) cc_final: 0.6879 (p90) REVERT: H 145 ARG cc_start: 0.7918 (mmm160) cc_final: 0.7676 (mmm160) REVERT: H 157 MET cc_start: 0.8233 (ptp) cc_final: 0.7747 (ppp) outliers start: 56 outliers final: 47 residues processed: 519 average time/residue: 0.3573 time to fit residues: 290.1262 Evaluate side-chains 527 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 477 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE 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 C residue 319 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 469 VAL 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 762 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 195 LEU 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 342 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 473 ILE 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 750 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 48 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 65 ASP 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 G residue 159 CYS Chi-restraints excluded: chain G residue 164 LYS 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 174 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** 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 = 0.4274 r_free = 0.4274 target = 0.185811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129768 restraints weight = 43369.996| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.97 r_work: 0.3412 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2818 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= 0.134 Angle : 0.666 11.214 34888 Z= 0.321 Chirality : 0.042 0.207 4012 Planarity : 0.004 0.055 4380 Dihedral : 8.141 172.761 3654 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.09 % Allowed : 22.02 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3184 helix: 1.36 (0.12), residues: 1820 sheet: -0.17 (0.35), residues: 256 loop : -0.72 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 733 HIS 0.005 0.001 HIS D 252 PHE 0.029 0.001 PHE C 172 TYR 0.031 0.001 TYR D 602 ARG 0.013 0.001 ARG G 145 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 1356) hydrogen bonds : angle 4.16155 ( 3921) covalent geometry : bond 0.00308 (25648) covalent geometry : angle 0.66631 (34888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15249.42 seconds wall clock time: 263 minutes 30.07 seconds (15810.07 seconds total)