Starting phenix.real_space_refine on Fri Sep 27 20:39:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_5777.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_5777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_5777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_5777.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5r_5777/09_2024/3j5r_5777.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} 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, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} 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, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} 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, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 8} 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: 9.82, per 1000 atoms: 0.56 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: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.95 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: 5.30 Time building geometry restraints manager: 5.47 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.950 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.140 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- 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= 0.706 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.008 0.001 TRP B 272 HIS 0.007 0.002 HIS C 289 PHE 0.024 0.001 PHE D 235 TYR 0.022 0.001 TYR B 309 ARG 0.005 0.001 ARG B 115 *********************** 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 fitting. rotamer outliers: 480 poor density : 429 time to evaluate : 2.087 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: 0.3212 time to fit residues: 365.7397 Evaluate side-chains 433 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 276 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 184 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN D 164 ASN D 289 HIS D 533 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 17908 Z= 0.376 Angle : 1.001 14.095 24344 Z= 0.519 Chirality : 0.049 0.416 2868 Planarity : 0.006 0.074 3072 Dihedral : 7.996 76.776 2548 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.90 % Favored : 95.23 % Rotamer: Outliers : 1.73 % Allowed : 3.52 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2308 helix: 0.47 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.43 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 697 HIS 0.004 0.002 HIS A 289 PHE 0.033 0.003 PHE B 434 TYR 0.042 0.003 TYR D 555 ARG 0.004 0.001 ARG C 557 *********************** 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 353 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 2.059 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: B 545 LEU cc_start: 0.7891 (tt) cc_final: 0.7517 (tp) REVERT: B 547 MET cc_start: 0.6819 (ptp) cc_final: 0.6502 (ptm) REVERT: B 549 TRP cc_start: 0.5802 (m100) cc_final: 0.5501 (m100) REVERT: B 550 THR cc_start: 0.8229 (p) cc_final: 0.8009 (t) REVERT: B 568 MET cc_start: 0.4900 (ptp) cc_final: 0.4551 (ptm) REVERT: A 545 LEU cc_start: 0.8024 (pp) cc_final: 0.7703 (pp) REVERT: A 547 MET cc_start: 0.7029 (ptp) cc_final: 0.6718 (ptm) REVERT: A 678 LEU cc_start: 0.7858 (tp) cc_final: 0.7565 (tp) REVERT: C 308 MET cc_start: 0.6952 (mtm) cc_final: 0.6490 (mpp) REVERT: C 547 MET cc_start: 0.6418 (ptp) cc_final: 0.5825 (ptp) REVERT: C 549 TRP cc_start: 0.5357 (m100) cc_final: 0.5095 (m100) REVERT: C 678 LEU cc_start: 0.7669 (tp) cc_final: 0.7121 (tp) REVERT: D 545 LEU cc_start: 0.7979 (pp) cc_final: 0.7521 (pp) REVERT: D 547 MET cc_start: 0.6786 (ptp) cc_final: 0.6116 (ptp) REVERT: D 550 THR cc_start: 0.8198 (p) cc_final: 0.7897 (t) outliers start: 29 outliers final: 4 residues processed: 348 average time/residue: 0.2414 time to fit residues: 136.0916 Evaluate side-chains 247 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 40.0000 chunk 66 optimal weight: 9.9990 chunk 178 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 59 optimal weight: 70.0000 chunk 214 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 212 optimal weight: 0.0770 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN B 652 ASN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN C 676 ASN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN D 652 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5097 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17908 Z= 0.254 Angle : 0.865 16.468 24344 Z= 0.442 Chirality : 0.044 0.324 2868 Planarity : 0.005 0.076 3072 Dihedral : 7.206 66.712 2548 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.76 % Favored : 93.72 % Rotamer: Outliers : 0.48 % Allowed : 6.03 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2308 helix: 0.74 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.15 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 549 HIS 0.005 0.001 HIS C 206 PHE 0.029 0.002 PHE C 543 TYR 0.028 0.002 TYR C 631 ARG 0.008 0.000 ARG C 557 *********************** 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 313 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 305 time to evaluate : 1.875 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: A 519 GLN cc_start: 0.6468 (mt0) cc_final: 0.6124 (mt0) REVERT: C 577 LEU cc_start: 0.6017 (pt) cc_final: 0.5748 (pt) REVERT: D 573 ILE cc_start: 0.7532 (pt) cc_final: 0.7272 (pt) REVERT: D 578 CYS cc_start: 0.5412 (p) cc_final: 0.5160 (p) outliers start: 8 outliers final: 1 residues processed: 312 average time/residue: 0.2358 time to fit residues: 119.1967 Evaluate side-chains 231 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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: 0.8980 chunk 161 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 0.1980 chunk 61 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN C 202 GLN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17908 Z= 0.203 Angle : 0.851 16.340 24344 Z= 0.423 Chirality : 0.042 0.287 2868 Planarity : 0.006 0.094 3072 Dihedral : 6.765 60.304 2548 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.50 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2308 helix: 0.64 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 549 HIS 0.004 0.001 HIS A 289 PHE 0.036 0.002 PHE A 543 TYR 0.027 0.002 TYR B 555 ARG 0.005 0.001 ARG B 428 *********************** 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 317 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 2.363 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 578 CYS cc_start: 0.5018 (p) cc_final: 0.4787 (p) REVERT: B 580 PHE cc_start: 0.5079 (t80) cc_final: 0.4874 (t80) REVERT: A 580 PHE cc_start: 0.4845 (t80) cc_final: 0.4621 (t80) REVERT: D 551 ASN cc_start: 0.7562 (m-40) cc_final: 0.6735 (m-40) REVERT: D 572 MET cc_start: 0.6288 (ptm) cc_final: 0.6039 (ptt) REVERT: D 578 CYS cc_start: 0.4988 (p) cc_final: 0.4762 (p) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2259 time to fit residues: 118.4982 Evaluate side-chains 242 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 194 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 60.0000 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** B 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17908 Z= 0.279 Angle : 0.809 18.511 24344 Z= 0.408 Chirality : 0.042 0.240 2868 Planarity : 0.005 0.088 3072 Dihedral : 6.509 53.865 2548 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.37 % Favored : 94.28 % Rotamer: Outliers : 0.24 % Allowed : 3.46 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2308 helix: 0.81 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.05 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP D 549 HIS 0.007 0.002 HIS B 206 PHE 0.026 0.002 PHE C 304 TYR 0.031 0.002 TYR C 554 ARG 0.008 0.000 ARG C 557 *********************** 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 284 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 280 time to evaluate : 1.996 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: B 578 CYS cc_start: 0.5405 (p) cc_final: 0.5200 (p) REVERT: A 550 THR cc_start: 0.8243 (p) cc_final: 0.8017 (p) REVERT: C 569 ILE cc_start: 0.7549 (pt) cc_final: 0.7231 (pt) REVERT: C 577 LEU cc_start: 0.5529 (pt) cc_final: 0.5309 (pt) REVERT: C 578 CYS cc_start: 0.5562 (p) cc_final: 0.5227 (p) REVERT: D 573 ILE cc_start: 0.7433 (pt) cc_final: 0.7187 (pt) REVERT: D 578 CYS cc_start: 0.5390 (p) cc_final: 0.5111 (p) outliers start: 4 outliers final: 0 residues processed: 284 average time/residue: 0.2251 time to fit residues: 105.8844 Evaluate side-chains 224 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5113 moved from start: 0.7834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17908 Z= 0.206 Angle : 0.793 18.130 24344 Z= 0.393 Chirality : 0.041 0.210 2868 Planarity : 0.005 0.079 3072 Dihedral : 6.145 51.018 2548 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.98 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.18), residues: 2308 helix: 0.88 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.03 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 697 HIS 0.003 0.001 HIS A 289 PHE 0.020 0.001 PHE B 543 TYR 0.021 0.002 TYR C 631 ARG 0.003 0.000 ARG C 557 *********************** 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 287 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.937 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: A 446 ILE cc_start: 0.8520 (pt) cc_final: 0.8250 (tp) REVERT: C 569 ILE cc_start: 0.7580 (pt) cc_final: 0.7281 (pt) REVERT: C 578 CYS cc_start: 0.5220 (p) cc_final: 0.4971 (p) REVERT: C 670 THR cc_start: 0.6095 (p) cc_final: 0.5786 (p) REVERT: D 573 ILE cc_start: 0.7545 (pt) cc_final: 0.7180 (pt) REVERT: D 577 LEU cc_start: 0.5806 (pt) cc_final: 0.5547 (pt) REVERT: D 641 THR cc_start: 0.8255 (p) cc_final: 0.8032 (t) REVERT: D 667 VAL cc_start: 0.7218 (m) cc_final: 0.6923 (m) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2310 time to fit residues: 109.8220 Evaluate side-chains 220 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 166 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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** ** 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** ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5131 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17908 Z= 0.213 Angle : 0.798 17.940 24344 Z= 0.397 Chirality : 0.041 0.183 2868 Planarity : 0.005 0.073 3072 Dihedral : 5.937 48.155 2548 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.33 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2308 helix: 0.91 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 697 HIS 0.002 0.001 HIS C 289 PHE 0.035 0.002 PHE A 543 TYR 0.021 0.002 TYR D 401 ARG 0.003 0.000 ARG A 557 *********************** 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 275 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.854 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: A 446 ILE cc_start: 0.8501 (pt) cc_final: 0.8050 (tp) REVERT: A 569 ILE cc_start: 0.7317 (pt) cc_final: 0.6956 (pt) REVERT: C 577 LEU cc_start: 0.5618 (pt) cc_final: 0.5356 (pt) REVERT: C 667 VAL cc_start: 0.6970 (t) cc_final: 0.6586 (t) REVERT: D 573 ILE cc_start: 0.7422 (pt) cc_final: 0.7189 (pt) REVERT: D 577 LEU cc_start: 0.5785 (pt) cc_final: 0.5577 (pt) REVERT: D 641 THR cc_start: 0.8261 (p) cc_final: 0.8041 (t) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2165 time to fit residues: 98.9378 Evaluate side-chains 207 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.8302 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= 0.199 Angle : 0.801 17.140 24344 Z= 0.398 Chirality : 0.041 0.181 2868 Planarity : 0.005 0.070 3072 Dihedral : 5.694 46.077 2548 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.63 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2308 helix: 0.95 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 549 HIS 0.002 0.001 HIS A 289 PHE 0.024 0.001 PHE B 543 TYR 0.021 0.001 TYR D 401 ARG 0.004 0.000 ARG B 557 *********************** 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 269 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.918 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 573 ILE cc_start: 0.7443 (pt) cc_final: 0.7169 (pt) REVERT: B 641 THR cc_start: 0.8276 (p) cc_final: 0.8072 (t) REVERT: A 446 ILE cc_start: 0.8493 (pt) cc_final: 0.8148 (tp) REVERT: A 580 PHE cc_start: 0.5117 (t80) cc_final: 0.4813 (t80) REVERT: C 667 VAL cc_start: 0.7072 (t) cc_final: 0.6770 (t) REVERT: C 670 THR cc_start: 0.6045 (p) cc_final: 0.5813 (p) REVERT: D 573 ILE cc_start: 0.7503 (pt) cc_final: 0.7212 (pt) REVERT: D 577 LEU cc_start: 0.5634 (pt) cc_final: 0.5368 (pt) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2228 time to fit residues: 99.7124 Evaluate side-chains 214 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 211 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 0.0370 chunk 65 optimal weight: 30.0000 chunk 191 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 139 optimal weight: 0.3980 chunk 224 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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** A 676 ASN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17908 Z= 0.181 Angle : 0.804 15.483 24344 Z= 0.399 Chirality : 0.042 0.174 2868 Planarity : 0.005 0.066 3072 Dihedral : 5.484 45.757 2548 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.85 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2308 helix: 0.91 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -1.28 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 549 HIS 0.002 0.001 HIS D 289 PHE 0.028 0.001 PHE B 247 TYR 0.023 0.001 TYR D 401 ARG 0.005 0.000 ARG B 557 *********************** 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 272 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.909 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: B 573 ILE cc_start: 0.7339 (pt) cc_final: 0.7066 (pt) REVERT: A 446 ILE cc_start: 0.8503 (pt) cc_final: 0.8153 (tp) REVERT: A 572 MET cc_start: 0.6575 (ptp) cc_final: 0.6286 (ptp) REVERT: A 573 ILE cc_start: 0.7340 (pt) cc_final: 0.7066 (pt) REVERT: C 573 ILE cc_start: 0.7277 (pt) cc_final: 0.6914 (pt) REVERT: D 573 ILE cc_start: 0.7424 (pt) cc_final: 0.7098 (pt) REVERT: D 577 LEU cc_start: 0.5352 (pt) cc_final: 0.4976 (pt) REVERT: D 642 ILE cc_start: 0.8022 (mt) cc_final: 0.7806 (mt) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2212 time to fit residues: 99.7931 Evaluate side-chains 212 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 144 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5121 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17908 Z= 0.204 Angle : 0.806 15.584 24344 Z= 0.403 Chirality : 0.042 0.218 2868 Planarity : 0.005 0.108 3072 Dihedral : 5.444 45.044 2548 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.89 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2308 helix: 1.02 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.42 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 549 HIS 0.002 0.001 HIS C 289 PHE 0.057 0.002 PHE B 438 TYR 0.021 0.002 TYR D 401 ARG 0.014 0.000 ARG C 557 ********************** 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 260 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.034 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: B 573 ILE cc_start: 0.7379 (pt) cc_final: 0.7113 (pt) REVERT: B 580 PHE cc_start: 0.5039 (t80) cc_final: 0.4771 (t80) REVERT: A 446 ILE cc_start: 0.8493 (pt) cc_final: 0.8109 (tp) REVERT: A 550 THR cc_start: 0.8249 (p) cc_final: 0.8019 (p) REVERT: A 573 ILE cc_start: 0.7217 (pt) cc_final: 0.6995 (pt) REVERT: C 547 MET cc_start: 0.5207 (ptt) cc_final: 0.4844 (ptt) REVERT: C 569 ILE cc_start: 0.7626 (pt) cc_final: 0.7263 (pt) REVERT: C 573 ILE cc_start: 0.7447 (pt) cc_final: 0.7083 (pt) REVERT: C 670 THR cc_start: 0.6186 (p) cc_final: 0.5940 (p) REVERT: C 675 LEU cc_start: 0.7993 (mt) cc_final: 0.7498 (mt) REVERT: D 573 ILE cc_start: 0.7404 (pt) cc_final: 0.7159 (pt) REVERT: D 580 PHE cc_start: 0.5067 (t80) cc_final: 0.4833 (t80) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2371 time to fit residues: 101.9698 Evaluate side-chains 207 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 301 ASN ** 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 164 ASN ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 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 = 0.3741 r_free = 0.3741 target = 0.106177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055211 restraints weight = 59292.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055233 restraints weight = 58441.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055233 restraints weight = 57893.516| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.9036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17908 Z= 0.281 Angle : 0.835 16.978 24344 Z= 0.429 Chirality : 0.043 0.203 2868 Planarity : 0.005 0.105 3072 Dihedral : 5.520 42.042 2548 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2308 helix: 0.81 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 549 HIS 0.003 0.001 HIS C 289 PHE 0.025 0.002 PHE C 543 TYR 0.021 0.002 TYR B 554 ARG 0.008 0.001 ARG C 242 =============================================================================== Job complete usr+sys time: 3493.62 seconds wall clock time: 63 minutes 43.48 seconds (3823.48 seconds total)