Starting phenix.real_space_refine on Wed Mar 4 20:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mts_23996/03_2026/7mts_23996.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 10258 2.51 5 N 2787 2.21 5 O 2914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16068 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6003 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 38, 'TRANS': 744} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5773 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 4 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 4, 'ASN:plan1': 2, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1412 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 1, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 10, 'ARG:plan': 6, 'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2438 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "E" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 364 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 1, 'ZQY': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.56, per 1000 atoms: 0.22 Number of scatterers: 16068 At special positions: 0 Unit cell: (109.33, 123.213, 252.501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 109 16.00 O 2914 8.00 N 2787 7.00 C 10258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.05 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 903 " - " ASN A 203 " " NAG B 902 " - " ASN B 203 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 881.3 milliseconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 24 sheets defined 43.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.797A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.941A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.841A pdb=" N ALA A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.554A pdb=" N GLU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.905A pdb=" N ALA A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 400 removed outlier: 3.559A pdb=" N VAL A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 565 through 592 removed outlier: 4.408A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.734A pdb=" N SER A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 625 removed outlier: 4.714A pdb=" N THR A 620 " --> pdb=" O CYS A 616 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 663 removed outlier: 4.063A pdb=" N LEU A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 677 through 701 removed outlier: 3.841A pdb=" N GLN A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 749 removed outlier: 3.595A pdb=" N THR A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 757 Processing helix chain 'A' and resid 758 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 786 through 819 removed outlier: 3.867A pdb=" N GLN A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'B' and resid 58 through 73 Processing helix chain 'B' and resid 94 through 107 removed outlier: 5.037A pdb=" N ASP B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.624A pdb=" N LEU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.791A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.658A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 230 removed outlier: 3.554A pdb=" N ALA B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.182A pdb=" N ALA B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.528A pdb=" N PHE B 348 " --> pdb=" O TRP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 400 removed outlier: 3.716A pdb=" N VAL B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 422 removed outlier: 3.757A pdb=" N TYR B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 426 removed outlier: 3.734A pdb=" N VAL B 426 " --> pdb=" O VAL B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 565 through 592 removed outlier: 4.590A pdb=" N GLY B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.574A pdb=" N SER B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 624 removed outlier: 4.316A pdb=" N THR B 620 " --> pdb=" O CYS B 616 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 624 " --> pdb=" O THR B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 660 removed outlier: 4.198A pdb=" N LEU B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE B 660 " --> pdb=" O ARG B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 701 removed outlier: 3.680A pdb=" N GLN B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 749 removed outlier: 3.690A pdb=" N LEU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 735 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 744 " --> pdb=" O ALA B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.163A pdb=" N PHE B 761 " --> pdb=" O ASN B 757 " (cutoff:3.500A) Proline residue: B 778 - end of helix removed outlier: 4.144A pdb=" N TYR B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 819 removed outlier: 3.576A pdb=" N GLN B 790 " --> pdb=" O ASP B 786 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 811 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.687A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.132A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 256 Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.158A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.650A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.647A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.535A pdb=" N CYS E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 42 " --> pdb=" O MET E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.507A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 33 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 140 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 35 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ILE A 163 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 241 removed outlier: 7.523A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 265 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TRP A 291 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 317 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A 293 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N LEU A 319 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 453 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR A 473 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 455 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 429 removed outlier: 3.670A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 512 Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 533 removed outlier: 3.514A pdb=" N LEU A 532 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 544 through 546 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.620A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 37 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 43 removed outlier: 4.688A pdb=" N GLN B 42 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 241 removed outlier: 6.042A pdb=" N VAL B 207 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 237 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR B 206 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 267 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 208 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE B 269 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 210 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TRP B 291 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE B 317 " --> pdb=" O TRP B 291 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 293 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N LEU B 319 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 453 " --> pdb=" O TYR B 473 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR B 473 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 455 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 428 through 429 removed outlier: 3.720A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 533 removed outlier: 6.824A pdb=" N THR B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 544 through 546 Processing sheet with id=AB7, first strand: chain 'B' and resid 705 through 708 Processing sheet with id=AB8, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.236A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.703A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 338 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 58 through 63 removed outlier: 7.350A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET D 61 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL D 71 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 63 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 69 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 88 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.230A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.830A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.537A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.944A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.876A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2220 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: 3.20 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5051 1.34 - 1.46: 3879 1.46 - 1.58: 7363 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 16434 Sorted by residual: bond pdb=" C1 ZQY A 901 " pdb=" C2 ZQY A 901 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 ZQY A 901 " pdb=" C6 ZQY A 901 " ideal model delta sigma weight residual 1.392 1.519 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C3 ZQY A 901 " pdb=" C4 ZQY A 901 " ideal model delta sigma weight residual 1.394 1.519 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C9 ZQY A 901 " pdb=" N1 ZQY A 901 " ideal model delta sigma weight residual 1.337 1.446 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N5 ZQY A 901 " pdb=" N6 ZQY A 901 " ideal model delta sigma weight residual 1.274 1.371 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 16429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 21744 1.99 - 3.98: 546 3.98 - 5.97: 75 5.97 - 7.96: 23 7.96 - 9.95: 5 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N GLU A 712 " pdb=" CA GLU A 712 " pdb=" C GLU A 712 " ideal model delta sigma weight residual 109.15 99.20 9.95 1.44e+00 4.82e-01 4.78e+01 angle pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" CD PRO B 711 " ideal model delta sigma weight residual 112.00 104.31 7.69 1.40e+00 5.10e-01 3.01e+01 angle pdb=" C GLU A 712 " pdb=" CA GLU A 712 " pdb=" CB GLU A 712 " ideal model delta sigma weight residual 110.67 118.62 -7.95 1.52e+00 4.33e-01 2.73e+01 angle pdb=" C ALA A 710 " pdb=" N PRO A 711 " pdb=" CA PRO A 711 " ideal model delta sigma weight residual 119.28 124.70 -5.42 1.10e+00 8.26e-01 2.42e+01 angle pdb=" CA ARG A 714 " pdb=" C ARG A 714 " pdb=" O ARG A 714 " ideal model delta sigma weight residual 120.55 115.53 5.02 1.06e+00 8.90e-01 2.24e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8900 17.93 - 35.85: 656 35.85 - 53.78: 109 53.78 - 71.70: 15 71.70 - 89.63: 18 Dihedral angle restraints: 9698 sinusoidal: 3480 harmonic: 6218 Sorted by residual: dihedral pdb=" CB CYS A 400 " pdb=" SG CYS A 400 " pdb=" SG CYS A 407 " pdb=" CB CYS A 407 " ideal model delta sinusoidal sigma weight residual 93.00 -177.37 -89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS B 540 " pdb=" SG CYS B 540 " pdb=" SG CYS B 553 " pdb=" CB CYS B 553 " ideal model delta sinusoidal sigma weight residual -86.00 -168.46 82.46 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual -86.00 -156.23 70.23 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 9695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2457 0.105 - 0.211: 108 0.211 - 0.316: 8 0.316 - 0.421: 0 0.421 - 0.526: 1 Chirality restraints: 2574 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 203 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA GLU B 516 " pdb=" N GLU B 516 " pdb=" C GLU B 516 " pdb=" CB GLU B 516 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA PRO B 711 " pdb=" N PRO B 711 " pdb=" C PRO B 711 " pdb=" CB PRO B 711 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2571 not shown) Planarity restraints: 2878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 903 " -0.164 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" C7 NAG A 903 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG A 903 " -0.121 2.00e-02 2.50e+03 pdb=" N2 NAG A 903 " 0.220 2.00e-02 2.50e+03 pdb=" O7 NAG A 903 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 902 " 0.073 2.00e-02 2.50e+03 5.99e-02 4.49e+01 pdb=" C7 NAG B 902 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B 902 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG B 902 " -0.095 2.00e-02 2.50e+03 pdb=" O7 NAG B 902 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 710 " 0.097 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO B 711 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO B 711 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 711 " 0.076 5.00e-02 4.00e+02 ... (remaining 2875 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2266 2.75 - 3.29: 14941 3.29 - 3.83: 24828 3.83 - 4.36: 28588 4.36 - 4.90: 51302 Nonbonded interactions: 121925 Sorted by model distance: nonbonded pdb=" OH TYR C 320 " pdb=" OD2 ASP C 341 " model vdw 2.213 3.040 nonbonded pdb=" O LEU B 686 " pdb=" OH TYR B 734 " model vdw 2.213 3.040 nonbonded pdb=" ND1 HIS D 142 " pdb=" OG SER D 161 " model vdw 2.233 3.120 nonbonded pdb=" O ALA A 630 " pdb=" OG1 THR A 633 " model vdw 2.235 3.040 nonbonded pdb=" O GLU B 508 " pdb=" NH1 ARG B 531 " model vdw 2.242 3.120 ... (remaining 121920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 358 or resid 360 through 419 or (r \ esid 420 and (name N or name CA or name C or name O or name CB )) or resid 421 t \ hrough 462 or resid 465 through 504 or (resid 505 through 506 and (name N or nam \ e CA or name C or name O or name CB )) or resid 507 through 512 or (resid 513 an \ d (name N or name CA or name C or name O or name CB )) or resid 514 through 549 \ or (resid 550 through 551 and (name N or name CA or name C or name O or name CB \ )) or resid 552 through 557 or (resid 558 through 559 and (name N or name CA or \ name C or name O or name CB )) or resid 560 or (resid 561 through 562 and (name \ N or name CA or name C or name O or name CB )) or resid 563 through 589 or (resi \ d 590 through 591 and (name N or name CA or name C or name O or name CB )) or re \ sid 592 through 598 or (resid 599 through 600 and (name N or name CA or name C o \ r name O or name CB )) or resid 601 through 602 or (resid 603 through 604 and (n \ ame N or name CA or name C or name O or name CB )) or resid 605 through 607 or ( \ resid 608 and (name N or name CA or name C or name O or name CB )) or resid 609 \ through 625 or (resid 626 and (name N or name CA or name C or name O or name CB \ )) or resid 627 through 640 or (resid 641 through 642 and (name N or name CA or \ name C or name O or name CB )) or resid 643 through 647 or (resid 648 through 64 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 650 through \ 654 or (resid 655 through 656 and (name N or name CA or name C or name O or name \ CB )) or resid 657 through 658 or (resid 659 through 661 and (name N or name CA \ or name C or name O or name CB )) or (resid 673 through 675 and (name N or name \ CA or name C or name O or name CB )) or resid 676 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 681 o \ r (resid 682 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 83 through 687 or (resid 688 and (name N or name CA or name C or name O or name \ CB )) or resid 689 through 708 or (resid 709 through 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 713 or (resid 714 through \ 716 and (name N or name CA or name C or name O or name CB )) or resid 717 throu \ gh 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 757 or (resid 758 through 759 and (name N or name CA or name \ C or name O or name CB )) or resid 760 through 765 or (resid 766 and (name N or \ name CA or name C or name O or name CB )) or resid 767 through 784 or (resid 785 \ and (name N or name CA or name C or name O or name CB )) or resid 786 through 8 \ 02 or (resid 803 and (name N or name CA or name C or name O or name CB )) or res \ id 804 through 817 or (resid 818 through 820 and (name N or name CA or name C or \ name O or name CB )) or resid 821 through 823 or resid 902 through 903)) selection = (chain 'B' and (resid 23 through 435 or (resid 436 and (name N or name CA or nam \ e C or name O or name CB )) or resid 437 through 475 or (resid 476 and (name N o \ r name CA or name C or name O or name CB )) or resid 477 through 505 or (resid 5 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 507 through \ 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or r \ esid 592 through 714 or (resid 715 through 716 and (name N or name CA or name C \ or name O or name CB )) or resid 717 through 902)) } 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: 8.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.007 0.138 16453 Z= 0.329 Angle : 0.778 9.951 22433 Z= 0.438 Chirality : 0.052 0.526 2574 Planarity : 0.007 0.143 2876 Dihedral : 13.165 87.771 5627 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2120 helix: 1.72 (0.18), residues: 842 sheet: -0.20 (0.25), residues: 394 loop : -0.91 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 499 TYR 0.021 0.002 TYR B 734 PHE 0.044 0.002 PHE A 554 TRP 0.032 0.002 TRP D 339 HIS 0.008 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00703 (16434) covalent geometry : angle 0.77402 (22393) SS BOND : bond 0.00512 ( 17) SS BOND : angle 1.51968 ( 34) hydrogen bonds : bond 0.16302 ( 762) hydrogen bonds : angle 5.50464 ( 2220) link_NAG-ASN : bond 0.01309 ( 2) link_NAG-ASN : angle 3.53776 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.505 Fit side-chains REVERT: D 102 THR cc_start: 0.8355 (m) cc_final: 0.8038 (p) REVERT: D 110 ASN cc_start: 0.8098 (m-40) cc_final: 0.7729 (m110) outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.1272 time to fit residues: 27.9818 Evaluate side-chains 133 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074825 restraints weight = 42495.059| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.19 r_work: 0.3030 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16453 Z= 0.131 Angle : 0.522 7.430 22433 Z= 0.281 Chirality : 0.042 0.139 2574 Planarity : 0.005 0.079 2876 Dihedral : 5.443 89.759 2369 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.57 % Allowed : 4.64 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 2120 helix: 2.14 (0.18), residues: 859 sheet: -0.27 (0.26), residues: 369 loop : -0.83 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 460 TYR 0.011 0.001 TYR D 124 PHE 0.016 0.001 PHE B 67 TRP 0.022 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00282 (16434) covalent geometry : angle 0.52005 (22393) SS BOND : bond 0.00202 ( 17) SS BOND : angle 1.15114 ( 34) hydrogen bonds : bond 0.05679 ( 762) hydrogen bonds : angle 4.35084 ( 2220) link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 1.12774 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.522 Fit side-chains REVERT: B 623 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.7377 (t80) REVERT: C 186 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8454 (tm-30) REVERT: D 110 ASN cc_start: 0.8368 (m-40) cc_final: 0.8060 (m-40) REVERT: D 127 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8603 (mtmm) REVERT: D 251 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7375 (mtt90) outliers start: 9 outliers final: 5 residues processed: 139 average time/residue: 0.1234 time to fit residues: 26.3315 Evaluate side-chains 132 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 168 optimal weight: 0.0010 chunk 129 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 99 optimal weight: 0.0370 chunk 143 optimal weight: 0.9980 overall best weight: 0.7866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075063 restraints weight = 43174.615| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.18 r_work: 0.3035 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16453 Z= 0.126 Angle : 0.495 7.140 22433 Z= 0.265 Chirality : 0.041 0.139 2574 Planarity : 0.004 0.064 2876 Dihedral : 5.154 84.757 2368 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.95 % Allowed : 6.55 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 2120 helix: 2.30 (0.18), residues: 869 sheet: -0.32 (0.26), residues: 378 loop : -0.87 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 314 TYR 0.011 0.001 TYR B 734 PHE 0.032 0.001 PHE A 554 TRP 0.018 0.001 TRP D 339 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00277 (16434) covalent geometry : angle 0.49421 (22393) SS BOND : bond 0.00178 ( 17) SS BOND : angle 0.87723 ( 34) hydrogen bonds : bond 0.05105 ( 762) hydrogen bonds : angle 4.08621 ( 2220) link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 0.93101 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.518 Fit side-chains REVERT: B 623 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7323 (t80) REVERT: C 186 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 205 ASP cc_start: 0.7775 (t0) cc_final: 0.7452 (t0) REVERT: D 212 ASP cc_start: 0.7653 (p0) cc_final: 0.7336 (p0) REVERT: D 233 CYS cc_start: 0.7738 (p) cc_final: 0.7499 (p) REVERT: D 251 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7630 (mtt90) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.1209 time to fit residues: 25.5199 Evaluate side-chains 141 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 91 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 43 optimal weight: 0.0070 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 0.0000 chunk 120 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 GLN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077460 restraints weight = 42851.702| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.17 r_work: 0.3090 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16453 Z= 0.087 Angle : 0.440 6.652 22433 Z= 0.235 Chirality : 0.040 0.149 2574 Planarity : 0.004 0.057 2876 Dihedral : 4.782 80.777 2368 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.14 % Allowed : 7.76 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2120 helix: 2.53 (0.18), residues: 870 sheet: -0.23 (0.25), residues: 386 loop : -0.83 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 713 TYR 0.009 0.001 TYR D 124 PHE 0.034 0.001 PHE A 554 TRP 0.013 0.001 TRP D 339 HIS 0.004 0.000 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00172 (16434) covalent geometry : angle 0.43978 (22393) SS BOND : bond 0.00124 ( 17) SS BOND : angle 0.67308 ( 34) hydrogen bonds : bond 0.03844 ( 762) hydrogen bonds : angle 3.75514 ( 2220) link_NAG-ASN : bond 0.00200 ( 2) link_NAG-ASN : angle 0.73608 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.655 Fit side-chains REVERT: B 623 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7106 (t80) REVERT: C 186 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 205 ASP cc_start: 0.7754 (t0) cc_final: 0.7336 (t0) REVERT: D 212 ASP cc_start: 0.7619 (p0) cc_final: 0.7297 (p0) REVERT: D 233 CYS cc_start: 0.7731 (p) cc_final: 0.7466 (p) REVERT: D 262 MET cc_start: 0.8862 (tpp) cc_final: 0.8467 (tpp) outliers start: 18 outliers final: 11 residues processed: 146 average time/residue: 0.1032 time to fit residues: 23.6150 Evaluate side-chains 143 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 187 optimal weight: 0.0000 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075089 restraints weight = 42614.765| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.17 r_work: 0.3036 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16453 Z= 0.136 Angle : 0.496 7.685 22433 Z= 0.264 Chirality : 0.041 0.158 2574 Planarity : 0.004 0.053 2876 Dihedral : 4.888 81.332 2368 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.14 % Allowed : 8.58 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2120 helix: 2.43 (0.18), residues: 871 sheet: -0.33 (0.25), residues: 392 loop : -0.80 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.012 0.001 TYR B 734 PHE 0.032 0.001 PHE A 554 TRP 0.013 0.001 TRP D 82 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00310 (16434) covalent geometry : angle 0.49549 (22393) SS BOND : bond 0.00196 ( 17) SS BOND : angle 0.78420 ( 34) hydrogen bonds : bond 0.04986 ( 762) hydrogen bonds : angle 3.89224 ( 2220) link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 1.03664 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.706 Fit side-chains REVERT: B 623 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7423 (t80) REVERT: C 186 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 205 ASP cc_start: 0.7875 (t0) cc_final: 0.7531 (t0) REVERT: D 233 CYS cc_start: 0.7692 (p) cc_final: 0.7383 (p) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1110 time to fit residues: 25.0127 Evaluate side-chains 144 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 45 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 184 optimal weight: 0.0670 chunk 180 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 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 = 0.3449 r_free = 0.3449 target = 0.089210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075599 restraints weight = 42728.320| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.19 r_work: 0.3048 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16453 Z= 0.113 Angle : 0.465 6.787 22433 Z= 0.248 Chirality : 0.040 0.144 2574 Planarity : 0.004 0.050 2876 Dihedral : 4.750 78.215 2368 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.46 % Allowed : 8.90 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 2120 helix: 2.47 (0.18), residues: 872 sheet: -0.29 (0.25), residues: 388 loop : -0.81 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 137 TYR 0.010 0.001 TYR B 734 PHE 0.035 0.001 PHE A 554 TRP 0.014 0.001 TRP D 339 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00251 (16434) covalent geometry : angle 0.46486 (22393) SS BOND : bond 0.00165 ( 17) SS BOND : angle 0.70147 ( 34) hydrogen bonds : bond 0.04503 ( 762) hydrogen bonds : angle 3.80037 ( 2220) link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 0.92060 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.592 Fit side-chains REVERT: A 375 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: B 623 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 186 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8445 (tm-30) REVERT: D 205 ASP cc_start: 0.7894 (t0) cc_final: 0.7576 (t0) REVERT: D 233 CYS cc_start: 0.7715 (p) cc_final: 0.7390 (p) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.1143 time to fit residues: 26.3263 Evaluate side-chains 146 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 4 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073174 restraints weight = 42544.548| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.22 r_work: 0.2990 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16453 Z= 0.192 Angle : 0.538 6.985 22433 Z= 0.287 Chirality : 0.043 0.148 2574 Planarity : 0.004 0.049 2876 Dihedral : 5.097 81.385 2368 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.59 % Allowed : 9.15 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 2120 helix: 2.22 (0.18), residues: 872 sheet: -0.46 (0.25), residues: 401 loop : -0.94 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.016 0.002 TYR B 734 PHE 0.034 0.002 PHE A 554 TRP 0.018 0.002 TRP D 339 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00449 (16434) covalent geometry : angle 0.53639 (22393) SS BOND : bond 0.00249 ( 17) SS BOND : angle 0.95753 ( 34) hydrogen bonds : bond 0.05883 ( 762) hydrogen bonds : angle 4.09820 ( 2220) link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 1.19283 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.487 Fit side-chains REVERT: A 375 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: B 623 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7707 (t80) REVERT: C 186 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 188 MET cc_start: 0.8665 (mtp) cc_final: 0.8173 (mtt) REVERT: D 205 ASP cc_start: 0.7995 (t0) cc_final: 0.7683 (t0) REVERT: D 212 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7329 (p0) REVERT: E 22 GLU cc_start: 0.7932 (tp30) cc_final: 0.7720 (tp30) outliers start: 25 outliers final: 18 residues processed: 147 average time/residue: 0.1232 time to fit residues: 27.9533 Evaluate side-chains 150 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 146 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 197 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 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 = 0.3411 r_free = 0.3411 target = 0.087189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.073546 restraints weight = 42686.105| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.19 r_work: 0.3005 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16453 Z= 0.164 Angle : 0.517 7.573 22433 Z= 0.276 Chirality : 0.042 0.150 2574 Planarity : 0.004 0.054 2876 Dihedral : 4.947 73.133 2368 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.34 % Allowed : 9.73 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 2120 helix: 2.24 (0.18), residues: 870 sheet: -0.46 (0.25), residues: 389 loop : -0.97 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 137 TYR 0.013 0.001 TYR B 734 PHE 0.036 0.001 PHE A 554 TRP 0.018 0.001 TRP D 339 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00382 (16434) covalent geometry : angle 0.51629 (22393) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.88068 ( 34) hydrogen bonds : bond 0.05530 ( 762) hydrogen bonds : angle 4.04898 ( 2220) link_NAG-ASN : bond 0.00131 ( 2) link_NAG-ASN : angle 1.10399 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.585 Fit side-chains REVERT: A 375 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: B 623 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7627 (t80) REVERT: D 188 MET cc_start: 0.8645 (mtp) cc_final: 0.8146 (mtt) REVERT: D 205 ASP cc_start: 0.7965 (t0) cc_final: 0.7649 (t0) REVERT: D 212 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7323 (p0) REVERT: D 233 CYS cc_start: 0.8431 (t) cc_final: 0.7290 (p) REVERT: D 262 MET cc_start: 0.8898 (tpp) cc_final: 0.8551 (tpp) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.1158 time to fit residues: 25.2708 Evaluate side-chains 147 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 73 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 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 = 0.3424 r_free = 0.3424 target = 0.087879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.074179 restraints weight = 42619.466| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.23 r_work: 0.3015 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16453 Z= 0.138 Angle : 0.497 8.013 22433 Z= 0.265 Chirality : 0.041 0.146 2574 Planarity : 0.004 0.053 2876 Dihedral : 4.884 74.113 2368 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.34 % Allowed : 9.85 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 2120 helix: 2.32 (0.18), residues: 870 sheet: -0.47 (0.25), residues: 391 loop : -0.96 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.012 0.001 TYR B 734 PHE 0.035 0.001 PHE A 554 TRP 0.016 0.001 TRP D 339 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00314 (16434) covalent geometry : angle 0.49579 (22393) SS BOND : bond 0.00201 ( 17) SS BOND : angle 0.81371 ( 34) hydrogen bonds : bond 0.05126 ( 762) hydrogen bonds : angle 3.95470 ( 2220) link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 1.05414 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.682 Fit side-chains REVERT: A 375 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: B 623 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7316 (t80) REVERT: D 188 MET cc_start: 0.8651 (mtp) cc_final: 0.8162 (mtt) REVERT: D 205 ASP cc_start: 0.7963 (t0) cc_final: 0.7641 (t0) REVERT: D 212 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7347 (p0) REVERT: D 262 MET cc_start: 0.8883 (tpp) cc_final: 0.8540 (tpp) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.1140 time to fit residues: 24.8107 Evaluate side-chains 145 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 111 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 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 = 0.3401 r_free = 0.3401 target = 0.086696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073027 restraints weight = 42618.284| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.22 r_work: 0.2987 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16453 Z= 0.197 Angle : 0.550 8.298 22433 Z= 0.293 Chirality : 0.043 0.151 2574 Planarity : 0.004 0.052 2876 Dihedral : 5.137 78.427 2368 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.21 % Allowed : 10.04 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2120 helix: 2.14 (0.18), residues: 870 sheet: -0.46 (0.25), residues: 399 loop : -1.09 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 656 TYR 0.015 0.001 TYR B 734 PHE 0.034 0.002 PHE A 554 TRP 0.018 0.002 TRP D 339 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00463 (16434) covalent geometry : angle 0.54911 (22393) SS BOND : bond 0.00258 ( 17) SS BOND : angle 0.97713 ( 34) hydrogen bonds : bond 0.05952 ( 762) hydrogen bonds : angle 4.13299 ( 2220) link_NAG-ASN : bond 0.00229 ( 2) link_NAG-ASN : angle 1.17893 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.590 Fit side-chains REVERT: B 623 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7826 (t80) REVERT: D 205 ASP cc_start: 0.7977 (t0) cc_final: 0.7665 (t0) REVERT: D 212 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7336 (p0) REVERT: D 262 MET cc_start: 0.8868 (tpp) cc_final: 0.8498 (tpp) outliers start: 19 outliers final: 17 residues processed: 137 average time/residue: 0.1113 time to fit residues: 23.9488 Evaluate side-chains 145 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 134 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 chunk 144 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 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 = 0.3429 r_free = 0.3429 target = 0.088177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074553 restraints weight = 42410.463| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.21 r_work: 0.3025 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16453 Z= 0.123 Angle : 0.487 8.240 22433 Z= 0.260 Chirality : 0.041 0.144 2574 Planarity : 0.004 0.054 2876 Dihedral : 4.873 75.884 2368 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.34 % Allowed : 10.04 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2120 helix: 2.37 (0.18), residues: 869 sheet: -0.43 (0.25), residues: 389 loop : -0.99 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.011 0.001 TYR B 734 PHE 0.035 0.001 PHE A 554 TRP 0.015 0.001 TRP D 339 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00274 (16434) covalent geometry : angle 0.48575 (22393) SS BOND : bond 0.00183 ( 17) SS BOND : angle 0.76632 ( 34) hydrogen bonds : bond 0.04851 ( 762) hydrogen bonds : angle 3.90873 ( 2220) link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 0.98741 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.65 seconds wall clock time: 75 minutes 52.76 seconds (4552.76 seconds total)