Starting phenix.real_space_refine on Thu Sep 18 13:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.map" model { file = "/net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j5r_5777/09_2025/3j5r_5777.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 11388 2.51 5 N 2904 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17564 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 208 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 208 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 208 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4338 Classifications: {'peptide': 581} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 88} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 560} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 14, 'HIS:plan': 4, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 53 Classifications: {'peptide': 11} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 4.56, per 1000 atoms: 0.26 Number of scatterers: 17564 At special positions: 0 Unit cell: (132.5, 132.5, 119.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3192 8.00 N 2904 7.00 C 11388 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 71.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.560A pdb=" N ILE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 406 through 413 removed outlier: 4.550A pdb=" N HIS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 413' Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.544A pdb=" N TRP B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 599 Processing helix chain 'B' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 670 Processing helix chain 'B' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.560A pdb=" N ILE A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 4.550A pdb=" N HIS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 412 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 413' Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.545A pdb=" N TRP A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.608A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 499 removed outlier: 3.793A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 599 Processing helix chain 'A' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 removed outlier: 3.989A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.312A pdb=" N ALA C 174 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 406 through 413 removed outlier: 4.549A pdb=" N HIS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 411 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 413' Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 533 removed outlier: 3.757A pdb=" N PHE C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 580 removed outlier: 3.530A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 599 Processing helix chain 'C' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 670 Processing helix chain 'C' and resid 670 through 687 removed outlier: 4.022A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN C 695 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP C 697 " --> pdb=" O SER C 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 355 Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 406 through 413 removed outlier: 4.549A pdb=" N HIS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 411 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET D 412 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 406 through 413' Processing helix chain 'D' and resid 417 through 429 removed outlier: 3.545A pdb=" N TRP D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.607A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 499 removed outlier: 3.794A pdb=" N ASP D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 533 removed outlier: 3.756A pdb=" N PHE D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 556 removed outlier: 3.980A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 580 removed outlier: 3.529A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 599 Processing helix chain 'D' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 670 through 687 removed outlier: 4.021A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 711 removed outlier: 3.988A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP D 697 " --> pdb=" O SER D 693 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'B' and resid 378 through 382 Processing sheet with id=B, first strand: chain 'A' and resid 378 through 382 Processing sheet with id=C, first strand: chain 'C' and resid 378 through 382 Processing sheet with id=D, first strand: chain 'D' and resid 378 through 382 1048 hydrogen bonds defined for protein. 3048 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: 3.13 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 5596 1.36 - 1.52: 7792 1.52 - 1.68: 4388 1.68 - 1.85: 108 1.85 - 2.01: 24 Bond restraints: 17908 Sorted by residual: bond pdb=" CG MET A 162 " pdb=" SD MET A 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.67e+01 bond pdb=" CG MET D 162 " pdb=" SD MET D 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.65e+01 bond pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 1.803 2.007 -0.204 2.50e-02 1.60e+03 6.64e+01 bond pdb=" CG MET C 162 " pdb=" SD MET C 162 " ideal model delta sigma weight residual 1.803 2.006 -0.203 2.50e-02 1.60e+03 6.60e+01 bond pdb=" CG MET A 214 " pdb=" SD MET A 214 " ideal model delta sigma weight residual 1.803 1.970 -0.167 2.50e-02 1.60e+03 4.48e+01 ... (remaining 17903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 23503 3.65 - 7.30: 769 7.30 - 10.94: 36 10.94 - 14.59: 16 14.59 - 18.24: 20 Bond angle restraints: 24344 Sorted by residual: angle pdb=" N VAL C 415 " pdb=" CA VAL C 415 " pdb=" C VAL C 415 " ideal model delta sigma weight residual 110.72 124.61 -13.89 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL A 415 " pdb=" CA VAL A 415 " pdb=" C VAL A 415 " ideal model delta sigma weight residual 110.72 124.61 -13.89 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL B 415 " pdb=" CA VAL B 415 " pdb=" C VAL B 415 " ideal model delta sigma weight residual 110.72 124.60 -13.88 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N VAL D 415 " pdb=" CA VAL D 415 " pdb=" C VAL D 415 " ideal model delta sigma weight residual 110.72 124.60 -13.88 1.01e+00 9.80e-01 1.89e+02 angle pdb=" N ASP B 383 " pdb=" CA ASP B 383 " pdb=" C ASP B 383 " ideal model delta sigma weight residual 111.07 121.74 -10.67 1.07e+00 8.73e-01 9.95e+01 ... (remaining 24339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 9326 24.92 - 49.84: 966 49.84 - 74.76: 172 74.76 - 99.68: 20 99.68 - 124.60: 8 Dihedral angle restraints: 10492 sinusoidal: 3584 harmonic: 6908 Sorted by residual: dihedral pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual 180.00 55.40 124.60 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY C 244 " pdb=" C GLY C 244 " pdb=" N PHE C 245 " pdb=" CA PHE C 245 " ideal model delta harmonic sigma weight residual 180.00 55.42 124.58 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY B 244 " pdb=" C GLY B 244 " pdb=" N PHE B 245 " pdb=" CA PHE B 245 " ideal model delta harmonic sigma weight residual 180.00 55.46 124.54 0 5.00e+00 4.00e-02 6.20e+02 ... (remaining 10489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2283 0.105 - 0.210: 493 0.210 - 0.315: 68 0.315 - 0.420: 16 0.420 - 0.526: 8 Chirality restraints: 2868 Sorted by residual: chirality pdb=" CA GLU A 249 " pdb=" N GLU A 249 " pdb=" C GLU A 249 " pdb=" CB GLU A 249 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA GLU B 249 " pdb=" N GLU B 249 " pdb=" C GLU B 249 " pdb=" CB GLU B 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 ... (remaining 2865 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 686 " 0.053 2.00e-02 2.50e+03 1.10e-01 1.21e+02 pdb=" C VAL D 686 " -0.190 2.00e-02 2.50e+03 pdb=" O VAL D 686 " 0.075 2.00e-02 2.50e+03 pdb=" N ASN D 687 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 686 " 0.053 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" C VAL B 686 " -0.190 2.00e-02 2.50e+03 pdb=" O VAL B 686 " 0.075 2.00e-02 2.50e+03 pdb=" N ASN B 687 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 686 " -0.053 2.00e-02 2.50e+03 1.10e-01 1.20e+02 pdb=" C VAL A 686 " 0.190 2.00e-02 2.50e+03 pdb=" O VAL A 686 " -0.075 2.00e-02 2.50e+03 pdb=" N ASN A 687 " -0.062 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 71 1.94 - 2.68: 1111 2.68 - 3.42: 27695 3.42 - 4.16: 42248 4.16 - 4.90: 72983 Nonbonded interactions: 144108 Sorted by model distance: nonbonded pdb=" OE1 GLN C 519 " pdb=" N GLY C 548 " model vdw 1.204 3.120 nonbonded pdb=" OE1 GLN A 519 " pdb=" N GLY A 548 " model vdw 1.204 3.120 nonbonded pdb=" OE1 GLN B 519 " pdb=" N GLY B 548 " model vdw 1.205 3.120 nonbonded pdb=" OE1 GLN D 519 " pdb=" N GLY D 548 " model vdw 1.205 3.120 nonbonded pdb=" O ASP B 601 " pdb=" ND2 ASN B 652 " model vdw 1.369 3.120 ... (remaining 144103 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 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 : 0.011 0.204 17908 Z= 0.640 Angle : 1.571 18.239 24344 Z= 1.086 Chirality : 0.091 0.526 2868 Planarity : 0.007 0.110 3072 Dihedral : 20.247 124.597 6052 Min Nonbonded Distance : 1.204 Molprobity Statistics. All-atom Clashscore : 84.36 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.80 % Favored : 90.99 % Rotamer: Outliers : 28.64 % Allowed : 15.75 % Favored : 55.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 1.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.17), residues: 2308 helix: 0.14 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.76 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 115 TYR 0.022 0.001 TYR B 309 PHE 0.024 0.001 PHE D 235 TRP 0.008 0.001 TRP B 272 HIS 0.007 0.002 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.01076 (17908) covalent geometry : angle 1.57118 (24344) hydrogen bonds : bond 0.26719 ( 1048) hydrogen bonds : angle 8.66466 ( 3048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 480 poor density : 429 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.2268 (OUTLIER) cc_final: -0.2576 (pt) REVERT: B 158 LEU cc_start: 0.3596 (OUTLIER) cc_final: 0.3356 (tp) REVERT: B 218 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7438 (p) REVERT: B 394 SER cc_start: 0.5460 (OUTLIER) cc_final: 0.5159 (t) REVERT: B 421 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5827 (tp) REVERT: B 545 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6584 (tp) REVERT: B 668 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6719 (pp) REVERT: B 681 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5306 (pp) REVERT: A 136 LEU cc_start: -0.2703 (OUTLIER) cc_final: -0.2958 (pt) REVERT: A 158 LEU cc_start: 0.3769 (OUTLIER) cc_final: 0.3560 (tp) REVERT: A 218 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 421 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5739 (tp) REVERT: A 668 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6758 (pp) REVERT: A 681 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5121 (pp) REVERT: C 136 LEU cc_start: -0.2953 (OUTLIER) cc_final: -0.3578 (pt) REVERT: C 218 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7647 (p) REVERT: C 421 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5786 (tp) REVERT: C 545 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6652 (tp) REVERT: C 647 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6668 (tm) REVERT: C 660 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7504 (pt) REVERT: C 668 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6030 (pp) REVERT: C 681 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.4823 (pp) REVERT: D 136 LEU cc_start: -0.2305 (OUTLIER) cc_final: -0.2626 (pt) REVERT: D 218 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7552 (p) REVERT: D 394 SER cc_start: 0.5436 (OUTLIER) cc_final: 0.5227 (t) REVERT: D 421 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5817 (tp) REVERT: D 668 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6748 (pp) REVERT: D 681 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5006 (pp) outliers start: 480 outliers final: 129 residues processed: 772 average time/residue: 0.1525 time to fit residues: 174.1368 Evaluate side-chains 433 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 276 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 289 HIS B 533 GLN ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 289 HIS C 533 GLN D 164 ASN D 289 HIS D 533 GLN ** D 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062027 restraints weight = 54233.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061785 restraints weight = 62414.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061732 restraints weight = 65653.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061726 restraints weight = 66102.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061726 restraints weight = 66160.347| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17908 Z= 0.284 Angle : 1.024 14.598 24344 Z= 0.527 Chirality : 0.049 0.377 2868 Planarity : 0.006 0.071 3072 Dihedral : 8.105 76.792 2548 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.03 % Favored : 95.10 % Rotamer: Outliers : 1.67 % Allowed : 4.24 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.17), residues: 2308 helix: 0.39 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 242 TYR 0.048 0.003 TYR B 555 PHE 0.037 0.003 PHE C 434 TRP 0.028 0.005 TRP C 272 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00583 (17908) covalent geometry : angle 1.02370 (24344) hydrogen bonds : bond 0.06480 ( 1048) hydrogen bonds : angle 5.80295 ( 3048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 MET cc_start: 0.9545 (mmp) cc_final: 0.9310 (mmm) REVERT: B 448 PHE cc_start: 0.9539 (t80) cc_final: 0.9111 (t80) REVERT: B 522 PHE cc_start: 0.9486 (m-80) cc_final: 0.9116 (m-80) REVERT: B 545 LEU cc_start: 0.9683 (tt) cc_final: 0.9418 (tp) REVERT: B 547 MET cc_start: 0.9099 (ptp) cc_final: 0.8866 (ptp) REVERT: B 549 TRP cc_start: 0.7495 (m100) cc_final: 0.6343 (m100) REVERT: B 580 PHE cc_start: 0.9188 (t80) cc_final: 0.8753 (t80) REVERT: B 591 PHE cc_start: 0.9380 (m-80) cc_final: 0.9112 (m-80) REVERT: B 642 ILE cc_start: 0.7397 (mt) cc_final: 0.7013 (mt) REVERT: A 445 MET cc_start: 0.9533 (mmp) cc_final: 0.9303 (mmm) REVERT: A 448 PHE cc_start: 0.9554 (t80) cc_final: 0.9100 (t80) REVERT: A 522 PHE cc_start: 0.9501 (m-80) cc_final: 0.9081 (m-80) REVERT: A 541 MET cc_start: 0.9666 (ptt) cc_final: 0.9449 (ppp) REVERT: A 547 MET cc_start: 0.9059 (ptp) cc_final: 0.8541 (ptp) REVERT: A 549 TRP cc_start: 0.7827 (m100) cc_final: 0.6836 (m100) REVERT: A 580 PHE cc_start: 0.9196 (t80) cc_final: 0.8717 (t80) REVERT: A 591 PHE cc_start: 0.9371 (m-80) cc_final: 0.9124 (m-80) REVERT: C 308 MET cc_start: 0.9556 (mtm) cc_final: 0.9271 (mpp) REVERT: C 448 PHE cc_start: 0.9519 (t80) cc_final: 0.9155 (t80) REVERT: C 522 PHE cc_start: 0.9361 (m-80) cc_final: 0.9112 (m-80) REVERT: C 549 TRP cc_start: 0.7430 (m100) cc_final: 0.6249 (m100) REVERT: C 568 MET cc_start: 0.9268 (ttp) cc_final: 0.9006 (ttm) REVERT: C 572 MET cc_start: 0.8138 (mtm) cc_final: 0.7712 (ptp) REVERT: C 580 PHE cc_start: 0.9579 (t80) cc_final: 0.9293 (t80) REVERT: C 635 LEU cc_start: 0.9669 (mm) cc_final: 0.9442 (pp) REVERT: D 445 MET cc_start: 0.9553 (mmp) cc_final: 0.9291 (mmm) REVERT: D 448 PHE cc_start: 0.9558 (t80) cc_final: 0.9083 (t80) REVERT: D 522 PHE cc_start: 0.9502 (m-80) cc_final: 0.9069 (m-80) REVERT: D 538 VAL cc_start: 0.9612 (OUTLIER) cc_final: 0.9219 (m) REVERT: D 543 PHE cc_start: 0.9508 (m-80) cc_final: 0.9270 (m-80) REVERT: D 545 LEU cc_start: 0.9657 (pp) cc_final: 0.9416 (pp) REVERT: D 547 MET cc_start: 0.9143 (ptp) cc_final: 0.8645 (ptp) REVERT: D 549 TRP cc_start: 0.7815 (m100) cc_final: 0.6874 (m100) REVERT: D 568 MET cc_start: 0.9624 (ttp) cc_final: 0.9345 (ttm) REVERT: D 569 ILE cc_start: 0.9433 (tt) cc_final: 0.9199 (pt) REVERT: D 572 MET cc_start: 0.9351 (mmp) cc_final: 0.8791 (ptm) REVERT: D 591 PHE cc_start: 0.9489 (m-80) cc_final: 0.9246 (m-80) REVERT: D 647 LEU cc_start: 0.9383 (tt) cc_final: 0.9106 (mp) outliers start: 28 outliers final: 6 residues processed: 347 average time/residue: 0.1130 time to fit residues: 64.9040 Evaluate side-chains 250 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 243 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 560 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN C 560 GLN C 676 ASN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 GLN D 560 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098961 restraints weight = 26242.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098888 restraints weight = 38867.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098888 restraints weight = 39608.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098888 restraints weight = 39608.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098888 restraints weight = 39608.064| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17908 Z= 0.180 Angle : 0.856 16.420 24344 Z= 0.436 Chirality : 0.044 0.327 2868 Planarity : 0.005 0.071 3072 Dihedral : 7.182 65.718 2548 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.72 % Favored : 93.76 % Rotamer: Outliers : 0.54 % Allowed : 4.30 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2308 helix: 0.69 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 557 TYR 0.031 0.002 TYR C 555 PHE 0.024 0.002 PHE C 304 TRP 0.023 0.002 TRP C 697 HIS 0.004 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00363 (17908) covalent geometry : angle 0.85634 (24344) hydrogen bonds : bond 0.05039 ( 1048) hydrogen bonds : angle 5.12184 ( 3048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 324 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.8362 (t-100) cc_final: 0.8021 (t-100) REVERT: B 522 PHE cc_start: 0.9509 (m-80) cc_final: 0.9099 (m-80) REVERT: B 547 MET cc_start: 0.9088 (ptp) cc_final: 0.8866 (ptp) REVERT: B 562 MET cc_start: 0.9282 (mmp) cc_final: 0.8976 (mmm) REVERT: B 568 MET cc_start: 0.9320 (ttp) cc_final: 0.8998 (ptm) REVERT: B 580 PHE cc_start: 0.9293 (t80) cc_final: 0.8694 (t80) REVERT: B 591 PHE cc_start: 0.9466 (m-80) cc_final: 0.9111 (m-80) REVERT: A 445 MET cc_start: 0.9498 (mmp) cc_final: 0.9182 (mmm) REVERT: A 448 PHE cc_start: 0.9548 (t80) cc_final: 0.9189 (t80) REVERT: A 522 PHE cc_start: 0.9464 (m-80) cc_final: 0.9098 (m-80) REVERT: A 547 MET cc_start: 0.8942 (ptp) cc_final: 0.8405 (ptm) REVERT: A 549 TRP cc_start: 0.7959 (m100) cc_final: 0.6890 (m100) REVERT: A 572 MET cc_start: 0.7581 (ptm) cc_final: 0.7169 (ptt) REVERT: A 580 PHE cc_start: 0.9301 (t80) cc_final: 0.8754 (t80) REVERT: A 591 PHE cc_start: 0.9454 (m-80) cc_final: 0.9152 (m-80) REVERT: C 309 TYR cc_start: 0.9742 (t80) cc_final: 0.9444 (t80) REVERT: C 426 TRP cc_start: 0.8312 (t-100) cc_final: 0.7962 (t-100) REVERT: C 448 PHE cc_start: 0.9579 (t80) cc_final: 0.9311 (t80) REVERT: C 515 LEU cc_start: 0.9660 (mm) cc_final: 0.9388 (mm) REVERT: C 549 TRP cc_start: 0.7874 (m100) cc_final: 0.7314 (m100) REVERT: C 568 MET cc_start: 0.9142 (ttp) cc_final: 0.8792 (ttm) REVERT: C 569 ILE cc_start: 0.8568 (pt) cc_final: 0.8270 (pt) REVERT: C 572 MET cc_start: 0.8118 (mtm) cc_final: 0.7644 (ptp) REVERT: C 580 PHE cc_start: 0.9591 (t80) cc_final: 0.9021 (t80) REVERT: C 591 PHE cc_start: 0.9426 (m-10) cc_final: 0.9224 (m-10) REVERT: C 659 PHE cc_start: 0.9145 (t80) cc_final: 0.8934 (t80) REVERT: D 426 TRP cc_start: 0.8195 (t-100) cc_final: 0.7923 (t-100) REVERT: D 445 MET cc_start: 0.9609 (mmp) cc_final: 0.9294 (mmm) REVERT: D 448 PHE cc_start: 0.9542 (t80) cc_final: 0.9126 (t80) REVERT: D 522 PHE cc_start: 0.9474 (m-80) cc_final: 0.9066 (m-80) REVERT: D 543 PHE cc_start: 0.9468 (m-80) cc_final: 0.9151 (m-80) REVERT: D 547 MET cc_start: 0.9049 (ptp) cc_final: 0.8403 (ptm) REVERT: D 549 TRP cc_start: 0.7899 (m100) cc_final: 0.6854 (m100) REVERT: D 568 MET cc_start: 0.9554 (ttp) cc_final: 0.9215 (ptm) REVERT: D 572 MET cc_start: 0.9238 (mmp) cc_final: 0.8672 (ptm) REVERT: D 591 PHE cc_start: 0.9508 (m-80) cc_final: 0.9104 (m-80) outliers start: 9 outliers final: 0 residues processed: 333 average time/residue: 0.1203 time to fit residues: 65.8435 Evaluate side-chains 243 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 30.0000 chunk 88 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 89 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 269 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 = 0.3779 r_free = 0.3779 target = 0.112547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062410 restraints weight = 58094.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062409 restraints weight = 65438.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062409 restraints weight = 65444.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062409 restraints weight = 65444.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062409 restraints weight = 65444.268| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17908 Z= 0.155 Angle : 0.830 16.491 24344 Z= 0.415 Chirality : 0.042 0.314 2868 Planarity : 0.006 0.096 3072 Dihedral : 6.756 59.495 2548 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.33 % Favored : 94.32 % Rotamer: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2308 helix: 0.66 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -1.32 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 428 TYR 0.027 0.002 TYR D 555 PHE 0.029 0.002 PHE B 543 TRP 0.020 0.002 TRP C 697 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00310 (17908) covalent geometry : angle 0.83017 (24344) hydrogen bonds : bond 0.04279 ( 1048) hydrogen bonds : angle 4.90562 ( 3048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 308 MET cc_start: 0.9312 (mmm) cc_final: 0.8978 (mmm) REVERT: B 426 TRP cc_start: 0.8585 (t-100) cc_final: 0.8293 (t-100) REVERT: B 434 PHE cc_start: 0.9755 (t80) cc_final: 0.9551 (t80) REVERT: B 438 PHE cc_start: 0.9600 (t80) cc_final: 0.9373 (t80) REVERT: B 445 MET cc_start: 0.9726 (mmp) cc_final: 0.9457 (mmm) REVERT: B 543 PHE cc_start: 0.9569 (m-80) cc_final: 0.9227 (m-80) REVERT: B 547 MET cc_start: 0.9200 (ptp) cc_final: 0.8937 (ptt) REVERT: B 565 TYR cc_start: 0.7846 (t80) cc_final: 0.7101 (t80) REVERT: B 568 MET cc_start: 0.9439 (ttp) cc_final: 0.9231 (ptm) REVERT: B 580 PHE cc_start: 0.9007 (t80) cc_final: 0.8370 (t80) REVERT: B 591 PHE cc_start: 0.9443 (m-80) cc_final: 0.9242 (m-80) REVERT: B 637 LEU cc_start: 0.9629 (mt) cc_final: 0.9376 (pp) REVERT: B 642 ILE cc_start: 0.7216 (mt) cc_final: 0.6796 (mt) REVERT: B 644 MET cc_start: 0.8673 (tpp) cc_final: 0.8280 (tpp) REVERT: A 308 MET cc_start: 0.9368 (mmm) cc_final: 0.9026 (mmm) REVERT: A 435 TYR cc_start: 0.9477 (m-10) cc_final: 0.9260 (m-80) REVERT: A 445 MET cc_start: 0.9466 (mmp) cc_final: 0.9132 (mmm) REVERT: A 448 PHE cc_start: 0.9705 (t80) cc_final: 0.9409 (t80) REVERT: A 522 PHE cc_start: 0.9402 (m-80) cc_final: 0.9086 (m-80) REVERT: A 543 PHE cc_start: 0.9596 (m-80) cc_final: 0.9279 (m-80) REVERT: A 547 MET cc_start: 0.9049 (ptp) cc_final: 0.8437 (ptm) REVERT: A 549 TRP cc_start: 0.8110 (m100) cc_final: 0.6898 (m100) REVERT: A 562 MET cc_start: 0.9487 (mmp) cc_final: 0.9232 (mmm) REVERT: A 580 PHE cc_start: 0.9069 (t80) cc_final: 0.8439 (t80) REVERT: A 591 PHE cc_start: 0.9289 (m-80) cc_final: 0.9064 (m-80) REVERT: C 426 TRP cc_start: 0.8613 (t-100) cc_final: 0.8227 (t-100) REVERT: C 524 LEU cc_start: 0.9699 (tt) cc_final: 0.9435 (mt) REVERT: C 549 TRP cc_start: 0.8342 (m100) cc_final: 0.7362 (m100) REVERT: C 568 MET cc_start: 0.9185 (ttp) cc_final: 0.8804 (ttm) REVERT: C 569 ILE cc_start: 0.8424 (pt) cc_final: 0.8110 (pt) REVERT: C 572 MET cc_start: 0.7921 (mtm) cc_final: 0.7352 (ptp) REVERT: C 580 PHE cc_start: 0.9432 (t80) cc_final: 0.8861 (t80) REVERT: C 659 PHE cc_start: 0.9211 (t80) cc_final: 0.8957 (t80) REVERT: D 308 MET cc_start: 0.9397 (mmm) cc_final: 0.9020 (mmm) REVERT: D 426 TRP cc_start: 0.8553 (t-100) cc_final: 0.8303 (t-100) REVERT: D 434 PHE cc_start: 0.9699 (t80) cc_final: 0.9475 (t80) REVERT: D 435 TYR cc_start: 0.9373 (m-10) cc_final: 0.9167 (m-80) REVERT: D 445 MET cc_start: 0.9616 (mmp) cc_final: 0.9305 (mmm) REVERT: D 448 PHE cc_start: 0.9712 (t80) cc_final: 0.9392 (t80) REVERT: D 543 PHE cc_start: 0.9448 (m-80) cc_final: 0.9123 (m-10) REVERT: D 549 TRP cc_start: 0.8192 (m100) cc_final: 0.6834 (m100) REVERT: D 562 MET cc_start: 0.9353 (mmp) cc_final: 0.9007 (mmm) REVERT: D 568 MET cc_start: 0.9539 (ttp) cc_final: 0.9131 (ptt) REVERT: D 569 ILE cc_start: 0.9444 (pt) cc_final: 0.9157 (pt) REVERT: D 572 MET cc_start: 0.9277 (mmp) cc_final: 0.8789 (mtp) REVERT: D 573 ILE cc_start: 0.8977 (pt) cc_final: 0.8730 (pt) REVERT: D 580 PHE cc_start: 0.8890 (t80) cc_final: 0.8283 (t80) REVERT: D 591 PHE cc_start: 0.9469 (m-80) cc_final: 0.9200 (m-80) REVERT: D 647 LEU cc_start: 0.9162 (tt) cc_final: 0.8849 (mp) outliers start: 2 outliers final: 1 residues processed: 320 average time/residue: 0.1074 time to fit residues: 57.8413 Evaluate side-chains 256 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 120 optimal weight: 50.0000 chunk 226 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 190 optimal weight: 10.0000 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060980 restraints weight = 59135.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060868 restraints weight = 67292.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060868 restraints weight = 67647.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060868 restraints weight = 67647.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060868 restraints weight = 67647.235| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17908 Z= 0.147 Angle : 0.778 17.131 24344 Z= 0.387 Chirality : 0.040 0.165 2868 Planarity : 0.005 0.088 3072 Dihedral : 6.188 50.659 2548 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.85 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2308 helix: 0.81 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.05 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.046 0.002 TYR B 435 PHE 0.025 0.001 PHE C 304 TRP 0.022 0.002 TRP C 697 HIS 0.003 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00305 (17908) covalent geometry : angle 0.77824 (24344) hydrogen bonds : bond 0.04057 ( 1048) hydrogen bonds : angle 4.69128 ( 3048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.8842 (t-100) cc_final: 0.8569 (t-100) REVERT: B 445 MET cc_start: 0.9743 (mmp) cc_final: 0.9336 (mmm) REVERT: B 543 PHE cc_start: 0.9581 (m-80) cc_final: 0.9267 (m-80) REVERT: B 552 MET cc_start: 0.9534 (tpt) cc_final: 0.9305 (mtp) REVERT: B 568 MET cc_start: 0.9401 (ttp) cc_final: 0.8947 (ptm) REVERT: B 580 PHE cc_start: 0.9015 (t80) cc_final: 0.8336 (t80) REVERT: B 637 LEU cc_start: 0.9593 (mt) cc_final: 0.9343 (pp) REVERT: B 642 ILE cc_start: 0.7022 (mt) cc_final: 0.6671 (mt) REVERT: A 445 MET cc_start: 0.9226 (mmp) cc_final: 0.9013 (mmm) REVERT: A 543 PHE cc_start: 0.9591 (m-80) cc_final: 0.9332 (m-80) REVERT: A 549 TRP cc_start: 0.8141 (m100) cc_final: 0.7294 (m100) REVERT: A 562 MET cc_start: 0.9273 (mmp) cc_final: 0.9064 (mmm) REVERT: A 580 PHE cc_start: 0.9022 (t80) cc_final: 0.8318 (t80) REVERT: A 591 PHE cc_start: 0.9377 (m-80) cc_final: 0.9087 (m-80) REVERT: C 426 TRP cc_start: 0.8762 (t-100) cc_final: 0.8368 (t-100) REVERT: C 445 MET cc_start: 0.9400 (mmp) cc_final: 0.9197 (mmm) REVERT: C 524 LEU cc_start: 0.9685 (tt) cc_final: 0.9415 (mt) REVERT: C 545 LEU cc_start: 0.9696 (pp) cc_final: 0.9486 (pp) REVERT: C 549 TRP cc_start: 0.8417 (m100) cc_final: 0.7648 (m100) REVERT: C 562 MET cc_start: 0.9373 (mmp) cc_final: 0.9155 (mmm) REVERT: C 568 MET cc_start: 0.9209 (ttp) cc_final: 0.8714 (ttp) REVERT: C 569 ILE cc_start: 0.8551 (pt) cc_final: 0.8197 (pt) REVERT: C 572 MET cc_start: 0.8016 (mtm) cc_final: 0.7784 (ptp) REVERT: C 591 PHE cc_start: 0.9349 (m-10) cc_final: 0.9107 (m-10) REVERT: C 659 PHE cc_start: 0.9257 (t80) cc_final: 0.8988 (t80) REVERT: D 308 MET cc_start: 0.9440 (mmm) cc_final: 0.9085 (mmm) REVERT: D 426 TRP cc_start: 0.8751 (t-100) cc_final: 0.8469 (t-100) REVERT: D 435 TYR cc_start: 0.9419 (m-10) cc_final: 0.9200 (m-80) REVERT: D 445 MET cc_start: 0.9551 (mmp) cc_final: 0.9309 (mmm) REVERT: D 543 PHE cc_start: 0.9486 (m-80) cc_final: 0.9139 (m-10) REVERT: D 549 TRP cc_start: 0.8382 (m100) cc_final: 0.7585 (m100) REVERT: D 568 MET cc_start: 0.9541 (ttp) cc_final: 0.9115 (ptt) REVERT: D 569 ILE cc_start: 0.9506 (pt) cc_final: 0.9161 (pt) REVERT: D 572 MET cc_start: 0.9271 (mmp) cc_final: 0.8781 (ptp) REVERT: D 573 ILE cc_start: 0.9002 (pt) cc_final: 0.8631 (pt) REVERT: D 580 PHE cc_start: 0.8903 (t80) cc_final: 0.8339 (t80) REVERT: D 591 PHE cc_start: 0.9471 (m-80) cc_final: 0.9242 (m-80) REVERT: D 644 MET cc_start: 0.8597 (tpp) cc_final: 0.8105 (tpp) REVERT: D 647 LEU cc_start: 0.9209 (tt) cc_final: 0.8936 (mp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1004 time to fit residues: 50.7006 Evaluate side-chains 247 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN B 676 ASN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN D 202 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059524 restraints weight = 59708.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059303 restraints weight = 69623.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059303 restraints weight = 72093.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059303 restraints weight = 72094.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059303 restraints weight = 72094.526| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.7798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17908 Z= 0.170 Angle : 0.775 17.820 24344 Z= 0.384 Chirality : 0.040 0.175 2868 Planarity : 0.005 0.075 3072 Dihedral : 5.932 51.434 2548 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.51 % Favored : 95.15 % Rotamer: Outliers : 0.18 % Allowed : 2.74 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2308 helix: 0.92 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -0.93 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 557 TYR 0.020 0.002 TYR C 631 PHE 0.020 0.002 PHE C 438 TRP 0.020 0.002 TRP C 697 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00341 (17908) covalent geometry : angle 0.77494 (24344) hydrogen bonds : bond 0.03973 ( 1048) hydrogen bonds : angle 4.57570 ( 3048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 TRP cc_start: 0.8867 (t-100) cc_final: 0.8618 (t-100) REVERT: B 438 PHE cc_start: 0.9611 (t80) cc_final: 0.9289 (t80) REVERT: B 445 MET cc_start: 0.9712 (mmp) cc_final: 0.9391 (mmm) REVERT: B 543 PHE cc_start: 0.9606 (m-80) cc_final: 0.9330 (m-80) REVERT: B 568 MET cc_start: 0.9364 (ttp) cc_final: 0.8994 (ptm) REVERT: B 580 PHE cc_start: 0.9010 (t80) cc_final: 0.8300 (t80) REVERT: B 642 ILE cc_start: 0.7325 (mt) cc_final: 0.7048 (mt) REVERT: B 644 MET cc_start: 0.8676 (tpp) cc_final: 0.8436 (tpp) REVERT: A 247 PHE cc_start: 0.9679 (p90) cc_final: 0.9297 (p90) REVERT: A 438 PHE cc_start: 0.9611 (t80) cc_final: 0.9355 (t80) REVERT: A 543 PHE cc_start: 0.9622 (m-80) cc_final: 0.9345 (m-80) REVERT: A 549 TRP cc_start: 0.8244 (m100) cc_final: 0.7451 (m100) REVERT: A 569 ILE cc_start: 0.8891 (pt) cc_final: 0.8688 (pt) REVERT: A 580 PHE cc_start: 0.9009 (t80) cc_final: 0.8301 (t80) REVERT: C 426 TRP cc_start: 0.8699 (t-100) cc_final: 0.8356 (t-100) REVERT: C 524 LEU cc_start: 0.9680 (tt) cc_final: 0.9425 (mt) REVERT: C 549 TRP cc_start: 0.8229 (m100) cc_final: 0.7692 (m100) REVERT: C 551 ASN cc_start: 0.8585 (m-40) cc_final: 0.8375 (m110) REVERT: C 568 MET cc_start: 0.9160 (ttp) cc_final: 0.8775 (ttm) REVERT: C 569 ILE cc_start: 0.8645 (pt) cc_final: 0.8297 (pt) REVERT: C 572 MET cc_start: 0.8494 (mtm) cc_final: 0.7967 (ptp) REVERT: C 580 PHE cc_start: 0.8975 (t80) cc_final: 0.8524 (t80) REVERT: C 659 PHE cc_start: 0.9301 (t80) cc_final: 0.9029 (t80) REVERT: D 308 MET cc_start: 0.9404 (mmm) cc_final: 0.9055 (mmm) REVERT: D 418 LEU cc_start: 0.9424 (mt) cc_final: 0.9221 (pp) REVERT: D 426 TRP cc_start: 0.8763 (t-100) cc_final: 0.8534 (t-100) REVERT: D 543 PHE cc_start: 0.9497 (m-80) cc_final: 0.9197 (m-10) REVERT: D 549 TRP cc_start: 0.8274 (m100) cc_final: 0.7666 (m100) REVERT: D 568 MET cc_start: 0.9517 (ttp) cc_final: 0.9096 (ptt) REVERT: D 569 ILE cc_start: 0.9506 (pt) cc_final: 0.9163 (pt) REVERT: D 572 MET cc_start: 0.9296 (mmp) cc_final: 0.8833 (ptp) REVERT: D 573 ILE cc_start: 0.9165 (pt) cc_final: 0.8797 (pt) REVERT: D 580 PHE cc_start: 0.8934 (t80) cc_final: 0.8381 (t80) REVERT: D 644 MET cc_start: 0.8665 (tpp) cc_final: 0.8154 (tpp) REVERT: D 647 LEU cc_start: 0.9019 (tt) cc_final: 0.8764 (mp) outliers start: 3 outliers final: 1 residues processed: 286 average time/residue: 0.1003 time to fit residues: 48.7120 Evaluate side-chains 237 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 177 optimal weight: 70.0000 chunk 74 optimal weight: 0.1980 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 269 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 = 0.3804 r_free = 0.3804 target = 0.109344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.059637 restraints weight = 59625.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059613 restraints weight = 58806.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059613 restraints weight = 58024.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059613 restraints weight = 58024.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.059613 restraints weight = 58024.736| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17908 Z= 0.156 Angle : 0.779 17.486 24344 Z= 0.385 Chirality : 0.040 0.175 2868 Planarity : 0.005 0.071 3072 Dihedral : 5.700 45.448 2548 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.07 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2308 helix: 1.05 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.021 0.002 TYR D 554 PHE 0.019 0.001 PHE D 438 TRP 0.018 0.002 TRP C 697 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00320 (17908) covalent geometry : angle 0.77881 (24344) hydrogen bonds : bond 0.03988 ( 1048) hydrogen bonds : angle 4.53603 ( 3048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.6811 (mt) cc_final: 0.6588 (mt) REVERT: B 247 PHE cc_start: 0.8652 (p90) cc_final: 0.8260 (p90) REVERT: B 438 PHE cc_start: 0.9303 (t80) cc_final: 0.9016 (t80) REVERT: B 545 LEU cc_start: 0.9383 (tp) cc_final: 0.9155 (tp) REVERT: B 568 MET cc_start: 0.9088 (ttp) cc_final: 0.8615 (ptm) REVERT: B 576 ASP cc_start: 0.8946 (t0) cc_final: 0.8206 (t0) REVERT: B 580 PHE cc_start: 0.8227 (t80) cc_final: 0.7495 (t80) REVERT: B 642 ILE cc_start: 0.5085 (mt) cc_final: 0.4839 (mt) REVERT: B 674 LEU cc_start: 0.9016 (mm) cc_final: 0.8815 (mm) REVERT: B 678 LEU cc_start: 0.9330 (tp) cc_final: 0.8987 (tp) REVERT: A 209 ILE cc_start: 0.7289 (mt) cc_final: 0.7037 (mt) REVERT: A 247 PHE cc_start: 0.8526 (p90) cc_final: 0.8153 (p90) REVERT: A 549 TRP cc_start: 0.6689 (m100) cc_final: 0.6198 (m100) REVERT: A 580 PHE cc_start: 0.8117 (t80) cc_final: 0.7283 (t80) REVERT: A 586 VAL cc_start: 0.8725 (t) cc_final: 0.8518 (t) REVERT: A 644 MET cc_start: 0.8223 (tpp) cc_final: 0.7907 (tpp) REVERT: A 660 ILE cc_start: 0.9268 (pt) cc_final: 0.8988 (pt) REVERT: C 524 LEU cc_start: 0.9327 (tt) cc_final: 0.9113 (mt) REVERT: C 568 MET cc_start: 0.8789 (ttp) cc_final: 0.8416 (ttm) REVERT: C 569 ILE cc_start: 0.7638 (pt) cc_final: 0.7200 (pt) REVERT: C 572 MET cc_start: 0.6386 (mtm) cc_final: 0.5564 (ptp) REVERT: C 662 LEU cc_start: 0.8762 (tt) cc_final: 0.8520 (tt) REVERT: D 426 TRP cc_start: 0.7707 (t-100) cc_final: 0.7501 (t-100) REVERT: D 549 TRP cc_start: 0.6760 (m100) cc_final: 0.6431 (m100) REVERT: D 568 MET cc_start: 0.9386 (ttp) cc_final: 0.9034 (ptt) REVERT: D 569 ILE cc_start: 0.9231 (pt) cc_final: 0.8879 (pt) REVERT: D 572 MET cc_start: 0.8688 (mmp) cc_final: 0.8354 (ptp) REVERT: D 573 ILE cc_start: 0.8573 (pt) cc_final: 0.8041 (pt) REVERT: D 580 PHE cc_start: 0.8037 (t80) cc_final: 0.7319 (t80) REVERT: D 644 MET cc_start: 0.8499 (tpp) cc_final: 0.8292 (tpp) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1001 time to fit residues: 47.0291 Evaluate side-chains 218 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 128 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 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 = 0.3752 r_free = 0.3752 target = 0.105659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055496 restraints weight = 59252.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055521 restraints weight = 59317.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055521 restraints weight = 59181.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055521 restraints weight = 59181.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055521 restraints weight = 59181.174| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.8428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17908 Z= 0.225 Angle : 0.829 18.536 24344 Z= 0.419 Chirality : 0.042 0.177 2868 Planarity : 0.005 0.066 3072 Dihedral : 5.738 44.349 2548 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.94 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.18), residues: 2308 helix: 0.98 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -1.13 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 579 TYR 0.024 0.002 TYR A 554 PHE 0.021 0.002 PHE A 245 TRP 0.042 0.003 TRP C 549 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00449 (17908) covalent geometry : angle 0.82863 (24344) hydrogen bonds : bond 0.04541 ( 1048) hydrogen bonds : angle 4.71515 ( 3048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 438 PHE cc_start: 0.9317 (t80) cc_final: 0.9043 (t80) REVERT: B 568 MET cc_start: 0.9066 (ttp) cc_final: 0.8652 (ptm) REVERT: B 576 ASP cc_start: 0.8792 (t0) cc_final: 0.8568 (t0) REVERT: B 580 PHE cc_start: 0.8284 (t80) cc_final: 0.7726 (t80) REVERT: A 209 ILE cc_start: 0.7653 (mt) cc_final: 0.7384 (mt) REVERT: A 247 PHE cc_start: 0.8588 (p90) cc_final: 0.8253 (p90) REVERT: A 549 TRP cc_start: 0.7159 (m100) cc_final: 0.6757 (m100) REVERT: A 565 TYR cc_start: 0.8015 (t80) cc_final: 0.7802 (t80) REVERT: A 580 PHE cc_start: 0.8256 (t80) cc_final: 0.7629 (t80) REVERT: A 644 MET cc_start: 0.8213 (tpp) cc_final: 0.7867 (tpp) REVERT: A 660 ILE cc_start: 0.9338 (pt) cc_final: 0.9108 (pt) REVERT: C 426 TRP cc_start: 0.7655 (t-100) cc_final: 0.7334 (t-100) REVERT: C 524 LEU cc_start: 0.9373 (tt) cc_final: 0.9148 (mt) REVERT: C 549 TRP cc_start: 0.6931 (m-90) cc_final: 0.5916 (m-90) REVERT: C 568 MET cc_start: 0.8752 (ttp) cc_final: 0.8359 (ttp) REVERT: C 569 ILE cc_start: 0.7824 (pt) cc_final: 0.7386 (pt) REVERT: C 572 MET cc_start: 0.6560 (mtm) cc_final: 0.6096 (ptp) REVERT: C 591 PHE cc_start: 0.9236 (m-10) cc_final: 0.8941 (m-10) REVERT: C 670 THR cc_start: 0.8194 (p) cc_final: 0.7699 (p) REVERT: D 438 PHE cc_start: 0.9177 (t80) cc_final: 0.8949 (t80) REVERT: D 549 TRP cc_start: 0.7324 (m100) cc_final: 0.7028 (m100) REVERT: D 568 MET cc_start: 0.9392 (ttp) cc_final: 0.9087 (ptp) REVERT: D 569 ILE cc_start: 0.9263 (pt) cc_final: 0.8893 (pt) REVERT: D 572 MET cc_start: 0.8887 (mmp) cc_final: 0.8505 (ptm) REVERT: D 573 ILE cc_start: 0.8727 (pt) cc_final: 0.8266 (pt) REVERT: D 580 PHE cc_start: 0.8259 (t80) cc_final: 0.7838 (t80) REVERT: D 644 MET cc_start: 0.8553 (tpp) cc_final: 0.8296 (tpp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1023 time to fit residues: 43.2543 Evaluate side-chains 202 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 80 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 176 optimal weight: 40.0000 chunk 106 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 173 optimal weight: 0.0670 chunk 215 optimal weight: 3.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 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 = 0.3786 r_free = 0.3786 target = 0.109832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057254 restraints weight = 55747.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057254 restraints weight = 55823.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057254 restraints weight = 55823.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057254 restraints weight = 55823.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057254 restraints weight = 55823.995| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.8560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17908 Z= 0.139 Angle : 0.796 16.069 24344 Z= 0.390 Chirality : 0.041 0.181 2868 Planarity : 0.005 0.066 3072 Dihedral : 5.430 41.501 2548 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.02 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.18), residues: 2308 helix: 1.04 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 557 TYR 0.024 0.002 TYR D 554 PHE 0.040 0.001 PHE C 543 TRP 0.033 0.002 TRP C 549 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00289 (17908) covalent geometry : angle 0.79606 (24344) hydrogen bonds : bond 0.03959 ( 1048) hydrogen bonds : angle 4.48089 ( 3048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.6541 (mt) cc_final: 0.6241 (mt) REVERT: B 247 PHE cc_start: 0.8446 (p90) cc_final: 0.8140 (p90) REVERT: B 426 TRP cc_start: 0.7830 (t-100) cc_final: 0.7605 (t-100) REVERT: B 438 PHE cc_start: 0.9311 (t80) cc_final: 0.9038 (t80) REVERT: B 545 LEU cc_start: 0.9298 (tp) cc_final: 0.9081 (tt) REVERT: B 547 MET cc_start: 0.8664 (ptt) cc_final: 0.8463 (ptt) REVERT: B 565 TYR cc_start: 0.7972 (t80) cc_final: 0.7587 (t80) REVERT: B 568 MET cc_start: 0.9115 (ttp) cc_final: 0.8763 (ptm) REVERT: B 569 ILE cc_start: 0.8906 (pt) cc_final: 0.8400 (pt) REVERT: B 573 ILE cc_start: 0.8538 (pt) cc_final: 0.8109 (pt) REVERT: B 580 PHE cc_start: 0.8186 (t80) cc_final: 0.7464 (t80) REVERT: B 586 VAL cc_start: 0.8753 (t) cc_final: 0.8469 (t) REVERT: A 209 ILE cc_start: 0.7347 (mt) cc_final: 0.7046 (mt) REVERT: A 247 PHE cc_start: 0.8371 (p90) cc_final: 0.8081 (p90) REVERT: A 580 PHE cc_start: 0.8089 (t80) cc_final: 0.7336 (t80) REVERT: A 660 ILE cc_start: 0.9246 (pt) cc_final: 0.9008 (pt) REVERT: A 678 LEU cc_start: 0.9281 (tp) cc_final: 0.9038 (tp) REVERT: C 426 TRP cc_start: 0.7467 (t-100) cc_final: 0.7153 (t-100) REVERT: C 524 LEU cc_start: 0.9359 (tt) cc_final: 0.9141 (mt) REVERT: C 568 MET cc_start: 0.8882 (ttp) cc_final: 0.8522 (ttp) REVERT: C 569 ILE cc_start: 0.7772 (pt) cc_final: 0.7281 (pt) REVERT: C 572 MET cc_start: 0.6205 (mtm) cc_final: 0.5910 (ptp) REVERT: C 580 PHE cc_start: 0.8237 (t80) cc_final: 0.7908 (t80) REVERT: C 660 ILE cc_start: 0.9271 (pt) cc_final: 0.9063 (pt) REVERT: D 209 ILE cc_start: 0.7120 (mt) cc_final: 0.6750 (mt) REVERT: D 247 PHE cc_start: 0.8302 (p90) cc_final: 0.7998 (p90) REVERT: D 426 TRP cc_start: 0.7900 (t-100) cc_final: 0.7623 (t-100) REVERT: D 549 TRP cc_start: 0.7043 (m100) cc_final: 0.6743 (m100) REVERT: D 568 MET cc_start: 0.9391 (ttp) cc_final: 0.9080 (ptp) REVERT: D 569 ILE cc_start: 0.9216 (pt) cc_final: 0.8812 (pt) REVERT: D 572 MET cc_start: 0.8741 (mmp) cc_final: 0.8375 (mtp) REVERT: D 573 ILE cc_start: 0.8633 (pt) cc_final: 0.8169 (pt) REVERT: D 580 PHE cc_start: 0.7971 (t80) cc_final: 0.7449 (t80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1012 time to fit residues: 45.2795 Evaluate side-chains 217 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 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 = 0.3784 r_free = 0.3784 target = 0.109888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057471 restraints weight = 55664.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057455 restraints weight = 55985.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057455 restraints weight = 55946.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057455 restraints weight = 55946.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057455 restraints weight = 55946.837| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17908 Z= 0.144 Angle : 0.784 15.168 24344 Z= 0.388 Chirality : 0.041 0.178 2868 Planarity : 0.005 0.062 3072 Dihedral : 5.290 41.614 2548 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.81 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2308 helix: 0.99 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 557 TYR 0.024 0.002 TYR D 554 PHE 0.025 0.001 PHE A 438 TRP 0.055 0.002 TRP A 549 HIS 0.002 0.000 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00299 (17908) covalent geometry : angle 0.78408 (24344) hydrogen bonds : bond 0.04035 ( 1048) hydrogen bonds : angle 4.43300 ( 3048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 ILE cc_start: 0.6874 (mt) cc_final: 0.6566 (mt) REVERT: B 247 PHE cc_start: 0.8485 (p90) cc_final: 0.8136 (p90) REVERT: B 438 PHE cc_start: 0.9319 (t80) cc_final: 0.9043 (t80) REVERT: B 545 LEU cc_start: 0.9344 (tp) cc_final: 0.9095 (tt) REVERT: B 568 MET cc_start: 0.9113 (ttp) cc_final: 0.8778 (ptm) REVERT: B 569 ILE cc_start: 0.8792 (pt) cc_final: 0.8453 (pt) REVERT: B 572 MET cc_start: 0.6666 (ptm) cc_final: 0.6135 (ptp) REVERT: B 580 PHE cc_start: 0.8245 (t80) cc_final: 0.7534 (t80) REVERT: B 586 VAL cc_start: 0.8717 (t) cc_final: 0.8437 (t) REVERT: B 591 PHE cc_start: 0.9295 (m-10) cc_final: 0.9092 (m-10) REVERT: B 660 ILE cc_start: 0.9422 (pt) cc_final: 0.9198 (pt) REVERT: A 209 ILE cc_start: 0.7803 (mt) cc_final: 0.7535 (mt) REVERT: A 247 PHE cc_start: 0.8404 (p90) cc_final: 0.8061 (p90) REVERT: A 549 TRP cc_start: 0.6634 (m-90) cc_final: 0.5998 (m-90) REVERT: A 580 PHE cc_start: 0.8100 (t80) cc_final: 0.7480 (t80) REVERT: A 660 ILE cc_start: 0.9305 (pt) cc_final: 0.9053 (pt) REVERT: C 426 TRP cc_start: 0.7585 (t-100) cc_final: 0.7250 (t-100) REVERT: C 524 LEU cc_start: 0.9420 (tt) cc_final: 0.9219 (mt) REVERT: C 549 TRP cc_start: 0.6468 (m-90) cc_final: 0.5749 (m-90) REVERT: C 568 MET cc_start: 0.8890 (ttp) cc_final: 0.8613 (ttm) REVERT: C 569 ILE cc_start: 0.7721 (pt) cc_final: 0.7370 (pt) REVERT: C 572 MET cc_start: 0.6663 (mtm) cc_final: 0.6203 (ptp) REVERT: C 580 PHE cc_start: 0.8278 (t80) cc_final: 0.7953 (t80) REVERT: C 586 VAL cc_start: 0.8794 (t) cc_final: 0.8586 (t) REVERT: C 660 ILE cc_start: 0.9393 (pt) cc_final: 0.9190 (pt) REVERT: C 662 LEU cc_start: 0.9004 (tt) cc_final: 0.8741 (tt) REVERT: D 209 ILE cc_start: 0.7406 (mt) cc_final: 0.7068 (mt) REVERT: D 247 PHE cc_start: 0.8375 (p90) cc_final: 0.8017 (p90) REVERT: D 438 PHE cc_start: 0.9370 (t80) cc_final: 0.9140 (t80) REVERT: D 549 TRP cc_start: 0.7181 (m100) cc_final: 0.6762 (m100) REVERT: D 568 MET cc_start: 0.9388 (ttp) cc_final: 0.9059 (ptp) REVERT: D 569 ILE cc_start: 0.9268 (pt) cc_final: 0.8849 (pt) REVERT: D 572 MET cc_start: 0.8758 (mmp) cc_final: 0.8355 (ptm) REVERT: D 573 ILE cc_start: 0.8680 (pt) cc_final: 0.8110 (pt) REVERT: D 580 PHE cc_start: 0.7984 (t80) cc_final: 0.7291 (t80) REVERT: D 666 TYR cc_start: 0.8983 (t80) cc_final: 0.8599 (t80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1033 time to fit residues: 46.1979 Evaluate side-chains 213 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 105 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 226 optimal weight: 0.2980 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 177 optimal weight: 60.0000 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 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 = 0.3767 r_free = 0.3767 target = 0.109168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056989 restraints weight = 56467.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056988 restraints weight = 57134.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056988 restraints weight = 57130.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056988 restraints weight = 57130.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056988 restraints weight = 57130.754| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.8909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17908 Z= 0.159 Angle : 0.781 15.081 24344 Z= 0.388 Chirality : 0.041 0.252 2868 Planarity : 0.005 0.062 3072 Dihedral : 5.209 40.015 2548 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.50 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2308 helix: 1.06 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -1.40 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.024 0.002 TYR D 554 PHE 0.017 0.001 PHE A 245 TRP 0.042 0.002 TRP C 549 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00326 (17908) covalent geometry : angle 0.78144 (24344) hydrogen bonds : bond 0.04054 ( 1048) hydrogen bonds : angle 4.47428 ( 3048) =============================================================================== Job complete usr+sys time: 3315.59 seconds wall clock time: 58 minutes 13.23 seconds (3493.23 seconds total)