Starting phenix.real_space_refine on Sat Jul 4 13:15:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.cif" model { file = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b16_11979/07_2026/7b16_11979.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13844 2.51 5 N 3456 2.21 5 O 3732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5222 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {' CA': 1, 'LPP': 1, 'SKQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.52, per 1000 atoms: 0.21 Number of scatterers: 21152 At special positions: 0 Unit cell: (139.23, 139.23, 139.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 O 3732 8.00 N 3456 7.00 C 13844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 686.0 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.656A pdb=" N TYR A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.826A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.549A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.637A pdb=" N HIS A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.842A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.904A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 215 through 234 removed outlier: 4.209A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.609A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.772A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 305 through 316 removed outlier: 3.552A pdb=" N LEU A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 removed outlier: 3.670A pdb=" N CYS A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.093A pdb=" N LEU A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.867A pdb=" N ILE A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 384 removed outlier: 4.311A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 Proline residue: A 408 - end of helix removed outlier: 3.546A pdb=" N GLY A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 458 removed outlier: 3.585A pdb=" N ILE A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 491 removed outlier: 3.659A pdb=" N PHE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.676A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 498 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.384A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 539 removed outlier: 4.127A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.985A pdb=" N VAL A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 592 through 610 removed outlier: 3.576A pdb=" N ALA A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 628 removed outlier: 3.835A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 698 through 720 removed outlier: 3.836A pdb=" N HIS A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 753 removed outlier: 3.657A pdb=" N PHE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.656A pdb=" N TYR B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.826A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.549A pdb=" N PHE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.637A pdb=" N HIS B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.842A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.904A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 215 through 234 removed outlier: 4.209A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.609A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 252 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.773A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.553A pdb=" N LEU B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.669A pdb=" N CYS B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 337 " --> pdb=" O CYS B 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 4.093A pdb=" N LEU B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.868A pdb=" N ILE B 359 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 384 removed outlier: 4.311A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 Proline residue: B 408 - end of helix removed outlier: 3.587A pdb=" N GLY B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 458 removed outlier: 3.585A pdb=" N ILE B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.659A pdb=" N PHE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.676A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 removed outlier: 4.384A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 539 removed outlier: 4.127A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 536 " --> pdb=" O ASN B 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.985A pdb=" N VAL B 583 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 584 " --> pdb=" O LEU B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'B' and resid 592 through 610 removed outlier: 3.576A pdb=" N ALA B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 628 removed outlier: 3.836A pdb=" N GLN B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 698 through 720 removed outlier: 3.837A pdb=" N HIS B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 753 removed outlier: 3.657A pdb=" N PHE B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.656A pdb=" N TYR C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.826A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.549A pdb=" N PHE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.637A pdb=" N HIS C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.842A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 165 removed outlier: 3.904A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 215 through 234 removed outlier: 4.209A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.609A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 252 " --> pdb=" O CYS C 248 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.772A pdb=" N ILE C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.553A pdb=" N LEU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 339 removed outlier: 3.669A pdb=" N CYS C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 348 removed outlier: 4.093A pdb=" N LEU C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.867A pdb=" N ILE C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 384 removed outlier: 4.311A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 Proline residue: C 408 - end of helix removed outlier: 3.546A pdb=" N GLY C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 458 removed outlier: 3.585A pdb=" N ILE C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.659A pdb=" N PHE C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 498 removed outlier: 3.676A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 498 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 512 removed outlier: 4.384A pdb=" N LEU C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 539 removed outlier: 4.127A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.985A pdb=" N VAL C 583 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 580 through 584' Processing helix chain 'C' and resid 592 through 610 removed outlier: 3.576A pdb=" N ALA C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 628 removed outlier: 3.836A pdb=" N GLN C 625 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 645 Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 698 through 720 removed outlier: 3.837A pdb=" N HIS C 703 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 753 removed outlier: 3.657A pdb=" N PHE C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.656A pdb=" N TYR D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.826A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.549A pdb=" N PHE D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.637A pdb=" N HIS D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 144 through 152 removed outlier: 3.842A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.904A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 4.209A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.609A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 252 " --> pdb=" O CYS D 248 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.772A pdb=" N ILE D 268 " --> pdb=" O GLU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.552A pdb=" N LEU D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 removed outlier: 3.670A pdb=" N CYS D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 337 " --> pdb=" O CYS D 333 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 348 removed outlier: 4.094A pdb=" N LEU D 343 " --> pdb=" O MET D 339 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 359 removed outlier: 3.867A pdb=" N ILE D 359 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 384 removed outlier: 4.311A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 Proline residue: D 408 - end of helix removed outlier: 3.547A pdb=" N GLY D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 458 removed outlier: 3.585A pdb=" N ILE D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 454 " --> pdb=" O SER D 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.659A pdb=" N PHE D 487 " --> pdb=" O ILE D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 498 removed outlier: 3.676A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 498 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 512 removed outlier: 4.384A pdb=" N LEU D 505 " --> pdb=" O HIS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 539 removed outlier: 4.127A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 536 " --> pdb=" O ASN D 532 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 537 " --> pdb=" O GLY D 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 580 through 584 removed outlier: 3.985A pdb=" N VAL D 583 " --> pdb=" O SER D 580 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 580 through 584' Processing helix chain 'D' and resid 592 through 610 removed outlier: 3.575A pdb=" N ALA D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 628 removed outlier: 3.835A pdb=" N GLN D 625 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 645 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 698 through 720 removed outlier: 3.836A pdb=" N HIS D 703 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 753 removed outlier: 3.657A pdb=" N PHE D 735 " --> pdb=" O THR D 731 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3552 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: 3.42 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 3324 1.31 - 1.45: 5989 1.45 - 1.59: 12127 1.59 - 1.73: 32 1.73 - 1.87: 180 Bond restraints: 21652 Sorted by residual: bond pdb=" O5 LPP A1003 " pdb=" P1 LPP A1003 " ideal model delta sigma weight residual 2.278 1.628 0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" O5 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 2.278 1.628 0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" O5 LPP C1001 " pdb=" P1 LPP C1001 " ideal model delta sigma weight residual 2.278 1.628 0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" O5 LPP B1001 " pdb=" P1 LPP B1001 " ideal model delta sigma weight residual 2.278 1.628 0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" O4 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 1.764 1.496 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 21647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.10: 29260 9.10 - 18.20: 24 18.20 - 27.30: 4 27.30 - 36.39: 8 36.39 - 45.49: 4 Bond angle restraints: 29300 Sorted by residual: angle pdb=" O4 LPP B1001 " pdb=" P1 LPP B1001 " pdb=" O5 LPP B1001 " ideal model delta sigma weight residual 62.99 108.48 -45.49 3.00e+00 1.11e-01 2.30e+02 angle pdb=" O4 LPP C1001 " pdb=" P1 LPP C1001 " pdb=" O5 LPP C1001 " ideal model delta sigma weight residual 62.99 108.46 -45.47 3.00e+00 1.11e-01 2.30e+02 angle pdb=" O4 LPP A1003 " pdb=" P1 LPP A1003 " pdb=" O5 LPP A1003 " ideal model delta sigma weight residual 62.99 108.46 -45.47 3.00e+00 1.11e-01 2.30e+02 angle pdb=" O4 LPP D1001 " pdb=" P1 LPP D1001 " pdb=" O5 LPP D1001 " ideal model delta sigma weight residual 62.99 108.46 -45.47 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C6 LPP D1001 " pdb=" O5 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 82.33 115.69 -33.36 3.00e+00 1.11e-01 1.24e+02 ... (remaining 29295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 12109 23.43 - 46.85: 640 46.85 - 70.28: 115 70.28 - 93.71: 16 93.71 - 117.13: 4 Dihedral angle restraints: 12884 sinusoidal: 5288 harmonic: 7596 Sorted by residual: dihedral pdb=" C18 SKQ B1002 " pdb=" C19 SKQ B1002 " pdb=" C20 SKQ B1002 " pdb=" C21 SKQ B1002 " ideal model delta sinusoidal sigma weight residual 63.74 -53.39 117.13 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C18 SKQ A1001 " pdb=" C19 SKQ A1001 " pdb=" C20 SKQ A1001 " pdb=" C21 SKQ A1001 " ideal model delta sinusoidal sigma weight residual 63.74 -53.38 117.12 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C18 SKQ C1002 " pdb=" C19 SKQ C1002 " pdb=" C20 SKQ C1002 " pdb=" C21 SKQ C1002 " ideal model delta sinusoidal sigma weight residual 63.74 -53.32 117.06 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 12881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3235 0.122 - 0.244: 37 0.244 - 0.366: 0 0.366 - 0.488: 4 0.488 - 0.610: 4 Chirality restraints: 3280 Sorted by residual: chirality pdb=" C16 SKQ A1001 " pdb=" C17 SKQ A1001 " pdb=" C21 SKQ A1001 " pdb=" N15 SKQ A1001 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C16 SKQ C1002 " pdb=" C17 SKQ C1002 " pdb=" C21 SKQ C1002 " pdb=" N15 SKQ C1002 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" C16 SKQ B1002 " pdb=" C17 SKQ B1002 " pdb=" C21 SKQ B1002 " pdb=" N15 SKQ B1002 " both_signs ideal model delta sigma weight residual False -2.38 -2.99 0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 3277 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 350 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO D 351 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 351 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 351 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 351 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 350 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 351 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 351 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 351 " 0.030 5.00e-02 4.00e+02 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4383 2.77 - 3.30: 19618 3.30 - 3.84: 32081 3.84 - 4.37: 38203 4.37 - 4.90: 67741 Nonbonded interactions: 162026 Sorted by model distance: nonbonded pdb=" NH2 ARG C 746 " pdb=" OE1 GLU D 748 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 746 " pdb=" OE1 GLU B 748 " model vdw 2.239 3.120 nonbonded pdb=" OE1 GLU A 748 " pdb=" NH2 ARG D 746 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG B 746 " pdb=" OE1 GLU C 748 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASP C 257 " pdb=" NE2 GLN C 303 " model vdw 2.243 3.120 ... (remaining 162021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 29 through 754) selection = (chain 'B' and resid 29 through 754) selection = (chain 'C' and resid 29 through 754) selection = (chain 'D' and resid 29 through 754) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.770 Find NCS groups from input model: 0.520 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.016 0.650 21652 Z= 0.742 Angle : 1.201 45.492 29300 Z= 0.514 Chirality : 0.053 0.610 3280 Planarity : 0.005 0.055 3620 Dihedral : 14.390 117.134 7940 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 (0.16), residues: 2516 helix: 0.16 (0.12), residues: 1792 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 511 TYR 0.016 0.002 TYR D 36 PHE 0.034 0.003 PHE B 519 TRP 0.015 0.002 TRP D 422 HIS 0.011 0.002 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.01564 / 0.74 (21652) covalent geometry : angle 1.20054 / 0.51 (29300) hydrogen bonds : bond 0.17341 / 11.37 ( 1204) hydrogen bonds : angle 5.01060 / 3.53 ( 3552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.761 Fit side-chains REVERT: A 429 TYR cc_start: 0.7758 (t80) cc_final: 0.7247 (t80) REVERT: A 737 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6498 (mt-10) REVERT: B 429 TYR cc_start: 0.7739 (t80) cc_final: 0.7236 (t80) REVERT: B 737 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6502 (mt-10) REVERT: C 429 TYR cc_start: 0.7757 (t80) cc_final: 0.7239 (t80) REVERT: C 737 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6503 (mt-10) REVERT: D 429 TYR cc_start: 0.7756 (t80) cc_final: 0.7241 (t80) REVERT: D 737 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6505 (mt-10) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1293 time to fit residues: 57.1008 Evaluate side-chains 224 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 702 ASN B 163 GLN B 702 ASN C 163 GLN C 702 ASN D 163 GLN D 702 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113045 restraints weight = 27353.619| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.28 r_work: 0.2860 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21652 Z= 0.120 Angle : 0.536 11.805 29300 Z= 0.259 Chirality : 0.036 0.124 3280 Planarity : 0.004 0.043 3620 Dihedral : 9.890 108.044 2976 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.88 % Allowed : 5.56 % Favored : 93.56 % 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: 0.13 (0.17), residues: 2516 helix: 0.96 (0.13), residues: 1844 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 360 TYR 0.011 0.001 TYR A 582 PHE 0.016 0.001 PHE D 340 TRP 0.016 0.001 TRP B 422 HIS 0.003 0.001 HIS D 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21652) covalent geometry : angle 0.53627 / 0.26 (29300) hydrogen bonds : bond 0.04359 / 2.88 ( 1204) hydrogen bonds : angle 3.44521 / 2.42 ( 3552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.803 Fit side-chains REVERT: A 336 ILE cc_start: 0.7881 (mm) cc_final: 0.7474 (mt) REVERT: A 429 TYR cc_start: 0.7389 (t80) cc_final: 0.6766 (t80) REVERT: B 336 ILE cc_start: 0.7947 (mm) cc_final: 0.7571 (mt) REVERT: B 429 TYR cc_start: 0.7399 (t80) cc_final: 0.6774 (t80) REVERT: C 336 ILE cc_start: 0.7950 (mm) cc_final: 0.7573 (mt) REVERT: C 429 TYR cc_start: 0.7393 (t80) cc_final: 0.6766 (t80) REVERT: D 336 ILE cc_start: 0.7943 (mm) cc_final: 0.7566 (mt) REVERT: D 429 TYR cc_start: 0.7398 (t80) cc_final: 0.6768 (t80) outliers start: 20 outliers final: 12 residues processed: 248 average time/residue: 0.1207 time to fit residues: 48.7485 Evaluate side-chains 205 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 205 optimal weight: 0.0370 chunk 27 optimal weight: 9.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 HIS A 532 ASN B 151 HIS B 532 ASN C 151 HIS C 532 ASN D 151 HIS D 532 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116095 restraints weight = 27470.343| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.05 r_work: 0.2884 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21652 Z= 0.094 Angle : 0.473 10.031 29300 Z= 0.229 Chirality : 0.035 0.130 3280 Planarity : 0.004 0.036 3620 Dihedral : 8.859 97.955 2976 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.06 % Allowed : 8.38 % Favored : 90.56 % 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: 0.91 (0.18), residues: 2516 helix: 1.51 (0.13), residues: 1856 sheet: None (None), residues: 0 loop : -2.06 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 746 TYR 0.009 0.001 TYR B 582 PHE 0.015 0.001 PHE A 340 TRP 0.009 0.001 TRP B 314 HIS 0.002 0.000 HIS A 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (21652) covalent geometry : angle 0.47292 / 0.23 (29300) hydrogen bonds : bond 0.03450 / 2.28 ( 1204) hydrogen bonds : angle 3.08941 / 2.16 ( 3552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.633 Fit side-chains REVERT: A 81 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 336 ILE cc_start: 0.7830 (mm) cc_final: 0.7454 (mt) REVERT: A 702 ASN cc_start: 0.8059 (m-40) cc_final: 0.7741 (m110) REVERT: B 81 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7708 (mt-10) REVERT: B 336 ILE cc_start: 0.7945 (mm) cc_final: 0.7515 (mt) REVERT: B 702 ASN cc_start: 0.8053 (m-40) cc_final: 0.7736 (m110) REVERT: C 81 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 336 ILE cc_start: 0.7940 (mm) cc_final: 0.7511 (mt) REVERT: C 702 ASN cc_start: 0.8047 (m-40) cc_final: 0.7730 (m110) REVERT: D 81 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7710 (mt-10) REVERT: D 336 ILE cc_start: 0.7944 (mm) cc_final: 0.7515 (mt) REVERT: D 702 ASN cc_start: 0.8052 (m-40) cc_final: 0.7736 (m110) outliers start: 24 outliers final: 24 residues processed: 243 average time/residue: 0.1245 time to fit residues: 47.7939 Evaluate side-chains 216 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 199 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3630 r_free = 0.3630 target = 0.143760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112225 restraints weight = 27576.593| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.15 r_work: 0.2855 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21652 Z= 0.127 Angle : 0.494 9.559 29300 Z= 0.241 Chirality : 0.036 0.132 3280 Planarity : 0.004 0.033 3620 Dihedral : 8.984 103.356 2976 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.50 % Allowed : 11.11 % Favored : 87.39 % 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: 1.18 (0.17), residues: 2516 helix: 1.67 (0.12), residues: 1860 sheet: None (None), residues: 0 loop : -1.86 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 360 TYR 0.010 0.001 TYR D 582 PHE 0.017 0.001 PHE A 340 TRP 0.011 0.001 TRP B 314 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21652) covalent geometry : angle 0.49397 / 0.24 (29300) hydrogen bonds : bond 0.04131 / 2.73 ( 1204) hydrogen bonds : angle 3.09322 / 2.17 ( 3552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 336 ILE cc_start: 0.8003 (mm) cc_final: 0.7601 (mt) REVERT: A 418 ILE cc_start: 0.8027 (tp) cc_final: 0.7698 (tp) REVERT: A 702 ASN cc_start: 0.8151 (m-40) cc_final: 0.7869 (m110) REVERT: A 737 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6446 (mt-10) REVERT: B 81 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7556 (mt-10) REVERT: B 336 ILE cc_start: 0.7958 (mm) cc_final: 0.7539 (mt) REVERT: B 418 ILE cc_start: 0.8017 (tp) cc_final: 0.7694 (tp) REVERT: B 702 ASN cc_start: 0.8149 (m-40) cc_final: 0.7865 (m110) REVERT: C 81 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7556 (mt-10) REVERT: C 336 ILE cc_start: 0.7952 (mm) cc_final: 0.7534 (mt) REVERT: C 418 ILE cc_start: 0.8018 (tp) cc_final: 0.7689 (tp) REVERT: C 702 ASN cc_start: 0.8146 (m-40) cc_final: 0.7862 (m110) REVERT: D 81 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 336 ILE cc_start: 0.7958 (mm) cc_final: 0.7539 (mt) REVERT: D 418 ILE cc_start: 0.8028 (tp) cc_final: 0.7699 (tp) REVERT: D 702 ASN cc_start: 0.8148 (m-40) cc_final: 0.7868 (m110) outliers start: 34 outliers final: 34 residues processed: 235 average time/residue: 0.1058 time to fit residues: 42.0938 Evaluate side-chains 231 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 652 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 202 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3627 r_free = 0.3627 target = 0.143634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111573 restraints weight = 27355.363| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.94 r_work: 0.2828 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21652 Z= 0.127 Angle : 0.488 9.548 29300 Z= 0.238 Chirality : 0.036 0.133 3280 Planarity : 0.004 0.032 3620 Dihedral : 8.935 103.660 2976 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.94 % Allowed : 11.68 % Favored : 86.38 % 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: 1.41 (0.17), residues: 2516 helix: 1.81 (0.12), residues: 1860 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 360 TYR 0.010 0.001 TYR C 582 PHE 0.016 0.001 PHE A 340 TRP 0.011 0.001 TRP D 314 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21652) covalent geometry : angle 0.48784 / 0.24 (29300) hydrogen bonds : bond 0.04060 / 2.69 ( 1204) hydrogen bonds : angle 3.05818 / 2.14 ( 3552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7503 (mt-10) REVERT: A 336 ILE cc_start: 0.7850 (mm) cc_final: 0.7439 (mt) REVERT: A 418 ILE cc_start: 0.7924 (tp) cc_final: 0.7675 (tp) REVERT: A 702 ASN cc_start: 0.8142 (m-40) cc_final: 0.7846 (m110) REVERT: A 723 ASP cc_start: 0.8271 (t0) cc_final: 0.7934 (t0) REVERT: B 81 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 336 ILE cc_start: 0.7954 (mm) cc_final: 0.7539 (mt) REVERT: B 418 ILE cc_start: 0.7910 (tp) cc_final: 0.7659 (tp) REVERT: B 702 ASN cc_start: 0.8146 (m-40) cc_final: 0.7848 (m110) REVERT: B 737 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6406 (mt-10) REVERT: C 81 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 336 ILE cc_start: 0.7949 (mm) cc_final: 0.7535 (mt) REVERT: C 418 ILE cc_start: 0.7920 (tp) cc_final: 0.7674 (tp) REVERT: C 702 ASN cc_start: 0.8140 (m-40) cc_final: 0.7841 (m110) REVERT: D 81 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7510 (mt-10) REVERT: D 336 ILE cc_start: 0.7948 (mm) cc_final: 0.7535 (mt) REVERT: D 418 ILE cc_start: 0.7930 (tp) cc_final: 0.7682 (tp) REVERT: D 702 ASN cc_start: 0.8141 (m-40) cc_final: 0.7847 (m110) REVERT: D 737 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6433 (mt-10) outliers start: 44 outliers final: 40 residues processed: 250 average time/residue: 0.1194 time to fit residues: 48.8528 Evaluate side-chains 228 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 113 optimal weight: 0.4980 chunk 131 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3601 r_free = 0.3601 target = 0.141488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.111895 restraints weight = 27425.150| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.25 r_work: 0.2802 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 21652 Z= 0.173 Angle : 0.541 9.796 29300 Z= 0.266 Chirality : 0.038 0.132 3280 Planarity : 0.004 0.033 3620 Dihedral : 9.118 106.018 2976 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.12 % Allowed : 11.33 % Favored : 86.55 % 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: 1.39 (0.17), residues: 2516 helix: 1.86 (0.12), residues: 1844 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 360 TYR 0.011 0.001 TYR A 582 PHE 0.018 0.002 PHE B 340 TRP 0.013 0.001 TRP C 314 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (21652) covalent geometry : angle 0.54090 / 0.27 (29300) hydrogen bonds : bond 0.04860 / 3.22 ( 1204) hydrogen bonds : angle 3.18549 / 2.23 ( 3552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 336 ILE cc_start: 0.7931 (mm) cc_final: 0.7533 (mt) REVERT: A 702 ASN cc_start: 0.8185 (m-40) cc_final: 0.7864 (m110) REVERT: A 737 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6572 (mt-10) REVERT: B 81 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 336 ILE cc_start: 0.7971 (mm) cc_final: 0.7561 (mt) REVERT: B 702 ASN cc_start: 0.8183 (m-40) cc_final: 0.7861 (m110) REVERT: B 737 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6536 (mt-10) REVERT: C 81 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 336 ILE cc_start: 0.7975 (mm) cc_final: 0.7565 (mt) REVERT: C 702 ASN cc_start: 0.8177 (m-40) cc_final: 0.7854 (m110) REVERT: D 81 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7492 (mt-10) REVERT: D 336 ILE cc_start: 0.7970 (mm) cc_final: 0.7564 (mt) REVERT: D 702 ASN cc_start: 0.8184 (m-40) cc_final: 0.7866 (m110) REVERT: D 737 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6548 (mt-10) outliers start: 48 outliers final: 48 residues processed: 248 average time/residue: 0.1224 time to fit residues: 49.5562 Evaluate side-chains 247 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 227 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 0.0570 chunk 246 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113387 restraints weight = 27363.302| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.20 r_work: 0.2816 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21652 Z= 0.128 Angle : 0.497 9.950 29300 Z= 0.244 Chirality : 0.036 0.130 3280 Planarity : 0.004 0.035 3620 Dihedral : 8.954 104.344 2976 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.29 % Allowed : 11.33 % Favored : 86.38 % 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: 1.65 (0.17), residues: 2516 helix: 2.00 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : -1.61 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 360 TYR 0.010 0.001 TYR B 582 PHE 0.016 0.001 PHE D 340 TRP 0.011 0.001 TRP C 314 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21652) covalent geometry : angle 0.49734 / 0.24 (29300) hydrogen bonds : bond 0.04117 / 2.73 ( 1204) hydrogen bonds : angle 3.09476 / 2.16 ( 3552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 336 ILE cc_start: 0.7834 (mm) cc_final: 0.7427 (mt) REVERT: A 339 MET cc_start: 0.7891 (ppp) cc_final: 0.7581 (ppp) REVERT: A 702 ASN cc_start: 0.8203 (m-40) cc_final: 0.7875 (m110) REVERT: A 723 ASP cc_start: 0.8304 (t0) cc_final: 0.8007 (t0) REVERT: A 737 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6545 (mt-10) REVERT: B 81 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 336 ILE cc_start: 0.7931 (mm) cc_final: 0.7500 (mt) REVERT: B 339 MET cc_start: 0.7898 (ppp) cc_final: 0.7588 (ppp) REVERT: B 702 ASN cc_start: 0.8209 (m-40) cc_final: 0.7880 (m110) REVERT: B 723 ASP cc_start: 0.8309 (t0) cc_final: 0.8017 (t0) REVERT: B 737 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6448 (mt-10) REVERT: C 81 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7606 (mt-10) REVERT: C 336 ILE cc_start: 0.7942 (mm) cc_final: 0.7508 (mt) REVERT: C 339 MET cc_start: 0.7899 (ppp) cc_final: 0.7589 (ppp) REVERT: C 702 ASN cc_start: 0.8203 (m-40) cc_final: 0.7873 (m110) REVERT: C 723 ASP cc_start: 0.8318 (t0) cc_final: 0.8022 (t0) REVERT: D 81 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7458 (mt-10) REVERT: D 336 ILE cc_start: 0.7927 (mm) cc_final: 0.7496 (mt) REVERT: D 339 MET cc_start: 0.7895 (ppp) cc_final: 0.7583 (ppp) REVERT: D 702 ASN cc_start: 0.8206 (m-40) cc_final: 0.7881 (m110) REVERT: D 723 ASP cc_start: 0.8314 (t0) cc_final: 0.8017 (t0) REVERT: D 737 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6469 (mt-10) outliers start: 52 outliers final: 52 residues processed: 255 average time/residue: 0.1191 time to fit residues: 49.8970 Evaluate side-chains 251 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 183 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.144141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112518 restraints weight = 27211.655| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.92 r_work: 0.2855 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21652 Z= 0.108 Angle : 0.480 9.286 29300 Z= 0.234 Chirality : 0.035 0.130 3280 Planarity : 0.003 0.035 3620 Dihedral : 8.776 102.002 2976 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.47 % Allowed : 11.46 % Favored : 86.07 % 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: 1.90 (0.17), residues: 2516 helix: 2.19 (0.12), residues: 1852 sheet: None (None), residues: 0 loop : -1.54 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 360 TYR 0.010 0.001 TYR C 582 PHE 0.016 0.001 PHE B 340 TRP 0.010 0.001 TRP B 314 HIS 0.003 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21652) covalent geometry : angle 0.47953 / 0.23 (29300) hydrogen bonds : bond 0.03638 / 2.41 ( 1204) hydrogen bonds : angle 3.01943 / 2.10 ( 3552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 336 ILE cc_start: 0.7795 (mm) cc_final: 0.7387 (mt) REVERT: A 702 ASN cc_start: 0.8122 (m-40) cc_final: 0.7804 (m110) REVERT: A 723 ASP cc_start: 0.8286 (t0) cc_final: 0.7996 (t0) REVERT: A 737 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6419 (mt-10) REVERT: B 81 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 336 ILE cc_start: 0.7882 (mm) cc_final: 0.7460 (mt) REVERT: B 702 ASN cc_start: 0.8123 (m-40) cc_final: 0.7803 (m110) REVERT: B 723 ASP cc_start: 0.8291 (t0) cc_final: 0.7999 (t0) REVERT: C 81 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 336 ILE cc_start: 0.7890 (mm) cc_final: 0.7467 (mt) REVERT: C 702 ASN cc_start: 0.8118 (m-40) cc_final: 0.7798 (m110) REVERT: C 723 ASP cc_start: 0.8296 (t0) cc_final: 0.8003 (t0) REVERT: D 81 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7394 (mt-10) REVERT: D 336 ILE cc_start: 0.7868 (mm) cc_final: 0.7448 (mt) REVERT: D 702 ASN cc_start: 0.8120 (m-40) cc_final: 0.7805 (m110) REVERT: D 723 ASP cc_start: 0.8290 (t0) cc_final: 0.8000 (t0) outliers start: 56 outliers final: 48 residues processed: 259 average time/residue: 0.1260 time to fit residues: 53.7894 Evaluate side-chains 255 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3622 r_free = 0.3622 target = 0.143014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099476 restraints weight = 27067.041| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.88 r_work: 0.2820 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 21652 Z= 0.190 Angle : 0.558 9.971 29300 Z= 0.275 Chirality : 0.038 0.134 3280 Planarity : 0.004 0.033 3620 Dihedral : 9.123 106.399 2976 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.12 % Allowed : 11.86 % Favored : 86.02 % 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: 1.60 (0.17), residues: 2516 helix: 2.03 (0.12), residues: 1844 sheet: None (None), residues: 0 loop : -1.79 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 360 TYR 0.011 0.001 TYR C 582 PHE 0.019 0.002 PHE A 340 TRP 0.013 0.001 TRP D 314 HIS 0.003 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (21652) covalent geometry : angle 0.55804 / 0.27 (29300) hydrogen bonds : bond 0.05052 / 3.35 ( 1204) hydrogen bonds : angle 3.18520 / 2.23 ( 3552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 336 ILE cc_start: 0.7914 (mm) cc_final: 0.7496 (mt) REVERT: A 702 ASN cc_start: 0.8165 (m-40) cc_final: 0.7859 (m110) REVERT: A 723 ASP cc_start: 0.8420 (t0) cc_final: 0.8167 (t0) REVERT: A 737 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6802 (mt-10) REVERT: B 81 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 336 ILE cc_start: 0.7941 (mm) cc_final: 0.7503 (mt) REVERT: B 702 ASN cc_start: 0.8166 (m-40) cc_final: 0.7858 (m110) REVERT: B 723 ASP cc_start: 0.8424 (t0) cc_final: 0.8180 (t0) REVERT: C 81 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C 336 ILE cc_start: 0.7946 (mm) cc_final: 0.7506 (mt) REVERT: C 702 ASN cc_start: 0.8159 (m-40) cc_final: 0.7854 (m110) REVERT: C 723 ASP cc_start: 0.8421 (t0) cc_final: 0.8173 (t0) REVERT: D 81 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7654 (mt-10) REVERT: D 336 ILE cc_start: 0.7946 (mm) cc_final: 0.7504 (mt) REVERT: D 702 ASN cc_start: 0.8166 (m-40) cc_final: 0.7864 (m110) REVERT: D 723 ASP cc_start: 0.8433 (t0) cc_final: 0.8184 (t0) REVERT: D 737 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6894 (mt-10) outliers start: 48 outliers final: 40 residues processed: 251 average time/residue: 0.1245 time to fit residues: 51.2481 Evaluate side-chains 246 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** 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 = 0.3638 r_free = 0.3638 target = 0.144785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114264 restraints weight = 27317.657| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.09 r_work: 0.2799 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21652 Z= 0.096 Angle : 0.492 12.382 29300 Z= 0.237 Chirality : 0.035 0.132 3280 Planarity : 0.003 0.035 3620 Dihedral : 8.722 101.407 2976 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.76 % Allowed : 12.26 % Favored : 85.98 % 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: 2.03 (0.18), residues: 2516 helix: 2.26 (0.12), residues: 1856 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 360 TYR 0.011 0.001 TYR C 582 PHE 0.015 0.001 PHE C 340 TRP 0.009 0.001 TRP D 314 HIS 0.002 0.000 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (21652) covalent geometry : angle 0.49202 / 0.24 (29300) hydrogen bonds : bond 0.03385 / 2.24 ( 1204) hydrogen bonds : angle 2.96714 / 2.08 ( 3552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 336 ILE cc_start: 0.7909 (mm) cc_final: 0.7481 (mt) REVERT: A 702 ASN cc_start: 0.8162 (m-40) cc_final: 0.7835 (m110) REVERT: A 723 ASP cc_start: 0.8356 (t0) cc_final: 0.8089 (t0) REVERT: A 737 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6557 (mt-10) REVERT: B 81 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 336 ILE cc_start: 0.7918 (mm) cc_final: 0.7489 (mt) REVERT: B 702 ASN cc_start: 0.8164 (m-40) cc_final: 0.7836 (m110) REVERT: B 723 ASP cc_start: 0.8357 (t0) cc_final: 0.8091 (t0) REVERT: C 81 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 336 ILE cc_start: 0.7923 (mm) cc_final: 0.7490 (mt) REVERT: C 702 ASN cc_start: 0.8157 (m-40) cc_final: 0.7828 (m110) REVERT: C 723 ASP cc_start: 0.8359 (t0) cc_final: 0.8091 (t0) REVERT: D 81 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7606 (mt-10) REVERT: D 336 ILE cc_start: 0.7907 (mm) cc_final: 0.7478 (mt) REVERT: D 702 ASN cc_start: 0.8159 (m-40) cc_final: 0.7836 (m110) REVERT: D 723 ASP cc_start: 0.8363 (t0) cc_final: 0.8092 (t0) outliers start: 40 outliers final: 36 residues processed: 242 average time/residue: 0.1278 time to fit residues: 50.8114 Evaluate side-chains 239 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 253 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115822 restraints weight = 27299.962| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.07 r_work: 0.2880 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21652 Z= 0.094 Angle : 0.486 12.162 29300 Z= 0.234 Chirality : 0.035 0.128 3280 Planarity : 0.003 0.034 3620 Dihedral : 8.605 99.485 2976 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.67 % 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: 2.24 (0.18), residues: 2516 helix: 2.41 (0.12), residues: 1860 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 360 TYR 0.009 0.001 TYR B 582 PHE 0.015 0.001 PHE B 340 TRP 0.010 0.001 TRP D 314 HIS 0.003 0.000 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (21652) covalent geometry : angle 0.48574 / 0.23 (29300) hydrogen bonds : bond 0.03200 / 2.11 ( 1204) hydrogen bonds : angle 2.93445 / 2.05 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.51 seconds wall clock time: 75 minutes 18.25 seconds (4518.25 seconds total)