Starting phenix.real_space_refine on Thu Feb 5 21:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.map" model { file = "/net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dd8_46760/02_2026/9dd8_46760.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 96 5.16 5 C 12513 2.51 5 N 3420 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19854 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4702 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4702 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4702 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 554} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.01, per 1000 atoms: 0.20 Number of scatterers: 19854 At special positions: 0 Unit cell: (145.25, 146.08, 180.94, 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 96 16.00 O 3825 8.00 N 3420 7.00 C 12513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.06 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.06 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.06 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 7 " " MAN D 4 " - " MAN D 5 " " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA K 3 " - " MAN K 7 " " MAN K 4 " - " MAN K 5 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 6 " " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 901 " - " ASN A 430 " " NAG A 902 " - " ASN A 674 " " NAG B 901 " - " ASN B 430 " " NAG B 902 " - " ASN B 674 " " NAG C 901 " - " ASN C 430 " " NAG C 902 " - " ASN C 674 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 398 " " NAG F 1 " - " ASN B 141 " " NAG G 1 " - " ASN B 398 " " NAG K 1 " - " ASN C 141 " " NAG O 1 " - " ASN C 398 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 804.1 milliseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 19.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.663A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.508A pdb=" N GLN A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Proline residue: A 516 - end of helix removed outlier: 4.289A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.939A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 698 removed outlier: 4.092A pdb=" N GLY A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.663A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 3.509A pdb=" N GLN B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Proline residue: B 516 - end of helix removed outlier: 4.291A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.937A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 698 removed outlier: 4.092A pdb=" N GLY B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.927A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.664A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.508A pdb=" N GLN C 507 " --> pdb=" O PHE C 503 " (cutoff:3.500A) Proline residue: C 516 - end of helix removed outlier: 4.290A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.937A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 698 removed outlier: 4.092A pdb=" N GLY C 698 " --> pdb=" O ILE C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.928A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.548A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 568 through 569 removed outlier: 3.803A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.991A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 448 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 175 removed outlier: 6.398A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 340 through 346 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 6.857A pdb=" N TYR A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A 658 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 649 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.357A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100G through 103 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB8, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.548A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 568 through 569 removed outlier: 6.912A pdb=" N VAL B 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL C 667 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.990A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 448 through 457 Processing sheet with id=AC2, first strand: chain 'B' and resid 157 through 175 removed outlier: 6.399A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 248 current: chain 'B' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 340 through 346 Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC4, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC5, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AC6, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 559 through 560 Processing sheet with id=AC8, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC9, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.857A pdb=" N TYR B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN B 658 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B 649 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100G through 103 Processing sheet with id=AD3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 13 current: chain 'M' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 53 through 54 current: chain 'M' and resid 97 through 98 Processing sheet with id=AD5, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.549A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.991A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 448 through 457 Processing sheet with id=AD7, first strand: chain 'C' and resid 157 through 175 removed outlier: 6.398A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 191 current: chain 'C' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 248 current: chain 'C' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 340 through 346 Processing sheet with id=AD8, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD9, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AE1, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AE2, first strand: chain 'C' and resid 375 through 379 Processing sheet with id=AE3, first strand: chain 'C' and resid 559 through 560 Processing sheet with id=AE4, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE5, first strand: chain 'C' and resid 638 through 643 removed outlier: 6.857A pdb=" N TYR C 647 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN C 658 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 649 " --> pdb=" O SER C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100G through 103 Processing sheet with id=AE8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'N' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 13 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 97 through 98 554 hydrogen bonds defined for protein. 1419 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: 3.09 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6159 1.34 - 1.46: 4158 1.46 - 1.58: 9867 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20334 Sorted by residual: bond pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.00e+01 bond pdb=" N VAL C 363 " pdb=" CA VAL C 363 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.22e-02 6.72e+03 1.00e+01 bond pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.71e+00 bond pdb=" N ILE C 413 " pdb=" CA ILE C 413 " ideal model delta sigma weight residual 1.459 1.500 -0.042 1.34e-02 5.57e+03 9.60e+00 bond pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.07e+00 ... (remaining 20329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 26879 2.52 - 5.04: 688 5.04 - 7.56: 57 7.56 - 10.08: 6 10.08 - 12.59: 3 Bond angle restraints: 27633 Sorted by residual: angle pdb=" N PHE I 100G" pdb=" CA PHE I 100G" pdb=" CB PHE I 100G" ideal model delta sigma weight residual 110.57 97.98 12.59 1.57e+00 4.06e-01 6.43e+01 angle pdb=" N PHE J 100G" pdb=" CA PHE J 100G" pdb=" CB PHE J 100G" ideal model delta sigma weight residual 110.57 98.00 12.57 1.57e+00 4.06e-01 6.41e+01 angle pdb=" N PHE H 100G" pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" ideal model delta sigma weight residual 110.57 98.04 12.53 1.57e+00 4.06e-01 6.37e+01 angle pdb=" CA ILE B 671 " pdb=" C ILE B 671 " pdb=" O ILE B 671 " ideal model delta sigma weight residual 122.63 118.05 4.58 8.70e-01 1.32e+00 2.77e+01 angle pdb=" CA ILE A 671 " pdb=" C ILE A 671 " pdb=" O ILE A 671 " ideal model delta sigma weight residual 122.63 118.09 4.54 8.70e-01 1.32e+00 2.73e+01 ... (remaining 27628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 11361 17.38 - 34.77: 865 34.77 - 52.15: 205 52.15 - 69.53: 49 69.53 - 86.91: 33 Dihedral angle restraints: 12513 sinusoidal: 5394 harmonic: 7119 Sorted by residual: dihedral pdb=" N PHE I 100G" pdb=" C PHE I 100G" pdb=" CA PHE I 100G" pdb=" CB PHE I 100G" ideal model delta harmonic sigma weight residual 122.80 109.16 13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" N PHE J 100G" pdb=" C PHE J 100G" pdb=" CA PHE J 100G" pdb=" CB PHE J 100G" ideal model delta harmonic sigma weight residual 122.80 109.18 13.62 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" N PHE H 100G" pdb=" C PHE H 100G" pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" ideal model delta harmonic sigma weight residual 122.80 109.26 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 12510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2757 0.085 - 0.170: 325 0.170 - 0.255: 26 0.255 - 0.340: 0 0.340 - 0.425: 3 Chirality restraints: 3111 Sorted by residual: chirality pdb=" C1 MAN K 6 " pdb=" O6 MAN K 4 " pdb=" C2 MAN K 6 " pdb=" O5 MAN K 6 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 1.03e+01 chirality pdb=" C1 MAN D 6 " pdb=" O6 MAN D 4 " pdb=" C2 MAN D 6 " pdb=" O5 MAN D 6 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.79e+00 chirality pdb=" C1 MAN F 6 " pdb=" O6 MAN F 4 " pdb=" C2 MAN F 6 " pdb=" O5 MAN F 6 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.61e+00 ... (remaining 3108 not shown) Planarity restraints: 3543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 674 " -0.032 2.00e-02 2.50e+03 7.55e-02 7.12e+01 pdb=" CG ASN B 674 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 674 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN B 674 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG B 902 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 674 " -0.032 2.00e-02 2.50e+03 7.53e-02 7.09e+01 pdb=" CG ASN A 674 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 674 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 674 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 674 " 0.032 2.00e-02 2.50e+03 7.53e-02 7.08e+01 pdb=" CG ASN C 674 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 674 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 674 " 0.131 2.00e-02 2.50e+03 pdb=" C1 NAG C 902 " -0.079 2.00e-02 2.50e+03 ... (remaining 3540 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1287 2.73 - 3.28: 19503 3.28 - 3.82: 32179 3.82 - 4.36: 40905 4.36 - 4.90: 70374 Nonbonded interactions: 164248 Sorted by model distance: nonbonded pdb=" OD2 ASP B 718 " pdb=" OG1 THR B 721 " model vdw 2.192 3.040 nonbonded pdb=" OD2 ASP A 718 " pdb=" OG1 THR A 721 " model vdw 2.194 3.040 nonbonded pdb=" OD2 ASP C 718 " pdb=" OG1 THR C 721 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR C 347 " pdb=" O PHE C 350 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR B 347 " pdb=" O PHE B 350 " model vdw 2.301 3.040 ... (remaining 164243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 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 : 0.005 0.147 20388 Z= 0.329 Angle : 0.945 12.594 27774 Z= 0.564 Chirality : 0.054 0.425 3111 Planarity : 0.007 0.113 3531 Dihedral : 13.684 86.914 7890 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2415 helix: -0.88 (0.29), residues: 294 sheet: -1.03 (0.18), residues: 783 loop : -0.50 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 178 TYR 0.018 0.001 TYR J 91 PHE 0.024 0.002 PHE H 100G TRP 0.008 0.001 TRP L 3 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00507 (20334) covalent geometry : angle 0.91006 (27633) SS BOND : bond 0.01129 ( 21) SS BOND : angle 1.68141 ( 42) hydrogen bonds : bond 0.22161 ( 554) hydrogen bonds : angle 10.15067 ( 1419) link_ALPHA1-3 : bond 0.01473 ( 6) link_ALPHA1-3 : angle 2.03700 ( 18) link_ALPHA1-6 : bond 0.02393 ( 6) link_ALPHA1-6 : angle 5.16992 ( 18) link_BETA1-4 : bond 0.00741 ( 9) link_BETA1-4 : angle 4.49011 ( 27) link_NAG-ASN : bond 0.07320 ( 12) link_NAG-ASN : angle 4.36300 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 TYR cc_start: 0.8760 (m-80) cc_final: 0.8462 (m-80) REVERT: A 612 LEU cc_start: 0.8923 (mm) cc_final: 0.8416 (tt) REVERT: H 72 ASP cc_start: 0.8444 (t0) cc_final: 0.8147 (t0) REVERT: H 85 ASP cc_start: 0.8931 (p0) cc_final: 0.8677 (p0) REVERT: B 177 HIS cc_start: 0.7558 (t70) cc_final: 0.7053 (t-170) REVERT: B 183 MET cc_start: 0.9005 (mmt) cc_final: 0.8619 (mmt) REVERT: I 18 LEU cc_start: 0.8144 (tm) cc_final: 0.7882 (tp) REVERT: I 72 ASP cc_start: 0.8347 (t0) cc_final: 0.7753 (t0) REVERT: I 85 ASP cc_start: 0.8562 (p0) cc_final: 0.8163 (p0) REVERT: M 81 GLU cc_start: 0.8655 (pm20) cc_final: 0.8441 (pm20) REVERT: M 105 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 677 MET cc_start: 0.8769 (mmt) cc_final: 0.8446 (mmm) REVERT: J 13 ARG cc_start: 0.8661 (mmp80) cc_final: 0.8372 (mmp80) REVERT: J 64 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8717 (tttp) REVERT: J 83 ARG cc_start: 0.7672 (mtm180) cc_final: 0.7319 (mtm180) REVERT: N 76 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8401 (mmmt) REVERT: N 77 ASN cc_start: 0.8382 (t0) cc_final: 0.8062 (t0) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1666 time to fit residues: 75.1102 Evaluate side-chains 197 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS A 534 HIS A 620 ASN H 55 ASN H 81 GLN L 37 GLN B 177 HIS B 433 HIS B 620 ASN C 433 HIS C 534 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051317 restraints weight = 56649.317| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.10 r_work: 0.2742 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20388 Z= 0.236 Angle : 0.661 12.993 27774 Z= 0.325 Chirality : 0.047 0.271 3111 Planarity : 0.005 0.038 3531 Dihedral : 5.366 54.803 3402 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.24 % Allowed : 11.35 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2415 helix: -0.30 (0.26), residues: 339 sheet: -0.82 (0.17), residues: 819 loop : -0.33 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 24 TYR 0.025 0.002 TYR B 380 PHE 0.021 0.002 PHE A 643 TRP 0.012 0.001 TRP C 354 HIS 0.008 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00550 (20334) covalent geometry : angle 0.62179 (27633) SS BOND : bond 0.00639 ( 21) SS BOND : angle 1.87543 ( 42) hydrogen bonds : bond 0.04419 ( 554) hydrogen bonds : angle 6.90252 ( 1419) link_ALPHA1-3 : bond 0.00841 ( 6) link_ALPHA1-3 : angle 2.09822 ( 18) link_ALPHA1-6 : bond 0.00701 ( 6) link_ALPHA1-6 : angle 2.51643 ( 18) link_BETA1-4 : bond 0.00575 ( 9) link_BETA1-4 : angle 3.55431 ( 27) link_NAG-ASN : bond 0.00682 ( 12) link_NAG-ASN : angle 4.66919 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9098 (mtp) cc_final: 0.8739 (mtp) REVERT: A 587 MET cc_start: 0.6583 (tmm) cc_final: 0.6049 (tmm) REVERT: A 597 TYR cc_start: 0.8871 (m-80) cc_final: 0.8455 (m-80) REVERT: A 620 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8293 (t0) REVERT: H 46 GLU cc_start: 0.8428 (tt0) cc_final: 0.8006 (tt0) REVERT: H 64 LYS cc_start: 0.9323 (ttmm) cc_final: 0.9118 (tppp) REVERT: H 72 ASP cc_start: 0.8257 (t0) cc_final: 0.7851 (t0) REVERT: H 85 ASP cc_start: 0.9088 (p0) cc_final: 0.8816 (p0) REVERT: L 4 MET cc_start: 0.8926 (mmm) cc_final: 0.8696 (mmm) REVERT: L 5 THR cc_start: 0.8982 (m) cc_final: 0.8714 (p) REVERT: I 53 ASP cc_start: 0.9139 (p0) cc_final: 0.8792 (p0) REVERT: I 55 ASN cc_start: 0.8879 (m-40) cc_final: 0.8621 (m110) REVERT: I 72 ASP cc_start: 0.8237 (t0) cc_final: 0.7748 (t0) REVERT: I 85 ASP cc_start: 0.8760 (p0) cc_final: 0.8542 (p0) REVERT: I 89 MET cc_start: 0.8470 (tpp) cc_final: 0.8149 (tpp) REVERT: M 5 THR cc_start: 0.9171 (m) cc_final: 0.8970 (p) REVERT: M 39 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7874 (mtt90) REVERT: M 81 GLU cc_start: 0.8916 (pm20) cc_final: 0.8513 (pm20) REVERT: M 105 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 601 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9136 (mm) REVERT: J 13 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8317 (mmp80) REVERT: J 81 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8279 (tm-30) REVERT: N 77 ASN cc_start: 0.8887 (t0) cc_final: 0.8579 (t0) REVERT: N 107 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7597 (ptmm) outliers start: 47 outliers final: 30 residues processed: 248 average time/residue: 0.1514 time to fit residues: 55.4014 Evaluate side-chains 217 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 169 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 HIS B 620 ASN M 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051839 restraints weight = 56605.095| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.10 r_work: 0.2793 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20388 Z= 0.129 Angle : 0.572 12.873 27774 Z= 0.277 Chirality : 0.044 0.286 3111 Planarity : 0.004 0.039 3531 Dihedral : 5.103 51.817 3402 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.05 % Allowed : 11.64 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2415 helix: 0.20 (0.28), residues: 339 sheet: -0.64 (0.17), residues: 840 loop : -0.15 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 16 TYR 0.027 0.001 TYR B 380 PHE 0.025 0.001 PHE B 643 TRP 0.019 0.001 TRP B 539 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00299 (20334) covalent geometry : angle 0.52580 (27633) SS BOND : bond 0.00232 ( 21) SS BOND : angle 2.19087 ( 42) hydrogen bonds : bond 0.03828 ( 554) hydrogen bonds : angle 6.46027 ( 1419) link_ALPHA1-3 : bond 0.00890 ( 6) link_ALPHA1-3 : angle 1.58798 ( 18) link_ALPHA1-6 : bond 0.00484 ( 6) link_ALPHA1-6 : angle 2.26770 ( 18) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 3.26033 ( 27) link_NAG-ASN : bond 0.00833 ( 12) link_NAG-ASN : angle 4.73460 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9134 (mtp) cc_final: 0.8369 (mtm) REVERT: A 587 MET cc_start: 0.6505 (tmm) cc_final: 0.5898 (tmm) REVERT: A 597 TYR cc_start: 0.8897 (m-80) cc_final: 0.8487 (m-80) REVERT: A 620 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8355 (t0) REVERT: H 72 ASP cc_start: 0.8227 (t0) cc_final: 0.7975 (t0) REVERT: H 85 ASP cc_start: 0.9117 (p0) cc_final: 0.8877 (p0) REVERT: L 5 THR cc_start: 0.9048 (m) cc_final: 0.8759 (p) REVERT: B 620 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8855 (t0) REVERT: I 53 ASP cc_start: 0.9081 (p0) cc_final: 0.8687 (p0) REVERT: I 55 ASN cc_start: 0.8871 (m-40) cc_final: 0.8526 (m110) REVERT: I 72 ASP cc_start: 0.8208 (t0) cc_final: 0.7709 (t0) REVERT: I 89 MET cc_start: 0.8486 (tpp) cc_final: 0.8151 (tpp) REVERT: M 39 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7864 (mtt90) REVERT: M 70 GLU cc_start: 0.8138 (tp30) cc_final: 0.7892 (tp30) REVERT: M 81 GLU cc_start: 0.8916 (pm20) cc_final: 0.8566 (pm20) REVERT: M 105 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8161 (mt-10) REVERT: J 13 ARG cc_start: 0.8728 (mmp80) cc_final: 0.8382 (mmp80) REVERT: J 81 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8250 (tm-30) REVERT: N 77 ASN cc_start: 0.8867 (t0) cc_final: 0.8601 (t0) outliers start: 43 outliers final: 27 residues processed: 233 average time/residue: 0.1545 time to fit residues: 53.7328 Evaluate side-chains 215 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 235 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 204 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN C 255 ASN C 311 HIS C 534 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050083 restraints weight = 56931.743| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.05 r_work: 0.2716 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20388 Z= 0.219 Angle : 0.609 12.887 27774 Z= 0.295 Chirality : 0.045 0.301 3111 Planarity : 0.004 0.038 3531 Dihedral : 5.290 52.039 3402 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.62 % Allowed : 11.83 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2415 helix: 0.58 (0.29), residues: 318 sheet: -0.64 (0.17), residues: 870 loop : 0.02 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.028 0.001 TYR B 380 PHE 0.024 0.001 PHE B 643 TRP 0.015 0.001 TRP B 528 HIS 0.018 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00516 (20334) covalent geometry : angle 0.56085 (27633) SS BOND : bond 0.00498 ( 21) SS BOND : angle 2.92978 ( 42) hydrogen bonds : bond 0.03737 ( 554) hydrogen bonds : angle 6.27380 ( 1419) link_ALPHA1-3 : bond 0.00692 ( 6) link_ALPHA1-3 : angle 1.83243 ( 18) link_ALPHA1-6 : bond 0.00455 ( 6) link_ALPHA1-6 : angle 2.24890 ( 18) link_BETA1-4 : bond 0.00516 ( 9) link_BETA1-4 : angle 3.38362 ( 27) link_NAG-ASN : bond 0.00802 ( 12) link_NAG-ASN : angle 4.70751 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9119 (mtp) cc_final: 0.8343 (mtm) REVERT: A 587 MET cc_start: 0.6589 (tmm) cc_final: 0.5941 (tmm) REVERT: A 597 TYR cc_start: 0.8908 (m-80) cc_final: 0.8500 (m-80) REVERT: A 620 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8414 (t0) REVERT: H 13 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8452 (mmp80) REVERT: H 72 ASP cc_start: 0.8208 (t0) cc_final: 0.7924 (t0) REVERT: L 5 THR cc_start: 0.9044 (m) cc_final: 0.8733 (p) REVERT: B 286 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8644 (pt0) REVERT: I 53 ASP cc_start: 0.9087 (p0) cc_final: 0.8660 (p0) REVERT: I 55 ASN cc_start: 0.9005 (m-40) cc_final: 0.8664 (m110) REVERT: I 72 ASP cc_start: 0.8192 (t0) cc_final: 0.7696 (t0) REVERT: I 85 ASP cc_start: 0.8826 (p0) cc_final: 0.8619 (p0) REVERT: I 89 MET cc_start: 0.8442 (tpp) cc_final: 0.8052 (tpp) REVERT: M 24 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7963 (ttm110) REVERT: M 39 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7881 (mtt90) REVERT: M 70 GLU cc_start: 0.8146 (tp30) cc_final: 0.7873 (tp30) REVERT: M 81 GLU cc_start: 0.8952 (pm20) cc_final: 0.8536 (pm20) REVERT: M 105 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8087 (mt-10) REVERT: C 601 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 83 ARG cc_start: 0.7257 (mtm180) cc_final: 0.6922 (mtm180) REVERT: N 76 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8396 (mmmt) REVERT: N 77 ASN cc_start: 0.8955 (t0) cc_final: 0.8746 (t0) outliers start: 55 outliers final: 37 residues processed: 231 average time/residue: 0.1651 time to fit residues: 56.0616 Evaluate side-chains 217 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 230 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 GLN A 534 HIS A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS J 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050460 restraints weight = 56581.956| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.06 r_work: 0.2721 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20388 Z= 0.163 Angle : 0.573 12.854 27774 Z= 0.277 Chirality : 0.044 0.294 3111 Planarity : 0.003 0.037 3531 Dihedral : 5.242 52.270 3402 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.53 % Allowed : 12.16 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2415 helix: 0.74 (0.29), residues: 318 sheet: -0.49 (0.17), residues: 879 loop : 0.08 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.028 0.001 TYR B 380 PHE 0.015 0.001 PHE B 643 TRP 0.009 0.001 TRP C 354 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00382 (20334) covalent geometry : angle 0.52462 (27633) SS BOND : bond 0.00357 ( 21) SS BOND : angle 2.58860 ( 42) hydrogen bonds : bond 0.03537 ( 554) hydrogen bonds : angle 6.09055 ( 1419) link_ALPHA1-3 : bond 0.00750 ( 6) link_ALPHA1-3 : angle 1.71842 ( 18) link_ALPHA1-6 : bond 0.00388 ( 6) link_ALPHA1-6 : angle 2.17144 ( 18) link_BETA1-4 : bond 0.00387 ( 9) link_BETA1-4 : angle 3.27553 ( 27) link_NAG-ASN : bond 0.00820 ( 12) link_NAG-ASN : angle 4.70543 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9102 (mtp) cc_final: 0.8330 (mtm) REVERT: A 587 MET cc_start: 0.6578 (tmm) cc_final: 0.5873 (tmm) REVERT: A 597 TYR cc_start: 0.8912 (m-80) cc_final: 0.8503 (m-80) REVERT: A 620 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8616 (t0) REVERT: H 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7884 (t0) REVERT: L 5 THR cc_start: 0.9050 (m) cc_final: 0.8796 (p) REVERT: B 534 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8637 (t70) REVERT: I 53 ASP cc_start: 0.9052 (p0) cc_final: 0.8696 (p0) REVERT: I 55 ASN cc_start: 0.8999 (m-40) cc_final: 0.8576 (m-40) REVERT: I 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7694 (t0) REVERT: I 89 MET cc_start: 0.8423 (tpp) cc_final: 0.8002 (tpp) REVERT: M 39 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7817 (mtt90) REVERT: M 70 GLU cc_start: 0.8139 (tp30) cc_final: 0.7898 (tp30) REVERT: M 81 GLU cc_start: 0.8944 (pm20) cc_final: 0.8534 (pm20) REVERT: M 105 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 601 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9217 (mm) REVERT: J 13 ARG cc_start: 0.8730 (mmp80) cc_final: 0.8381 (mmp80) REVERT: J 82 MET cc_start: 0.8821 (mtt) cc_final: 0.8098 (mtm) REVERT: N 76 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8413 (mmmt) outliers start: 53 outliers final: 35 residues processed: 228 average time/residue: 0.1661 time to fit residues: 55.0999 Evaluate side-chains 218 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 54 optimal weight: 0.0070 chunk 233 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051327 restraints weight = 56015.928| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.05 r_work: 0.2738 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20388 Z= 0.124 Angle : 0.561 12.828 27774 Z= 0.273 Chirality : 0.043 0.285 3111 Planarity : 0.003 0.039 3531 Dihedral : 5.119 51.768 3402 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.29 % Allowed : 12.59 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2415 helix: 0.42 (0.29), residues: 342 sheet: -0.46 (0.17), residues: 864 loop : 0.03 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 328 TYR 0.028 0.001 TYR B 380 PHE 0.015 0.001 PHE B 643 TRP 0.009 0.001 TRP B 528 HIS 0.005 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00290 (20334) covalent geometry : angle 0.51015 (27633) SS BOND : bond 0.00493 ( 21) SS BOND : angle 2.98343 ( 42) hydrogen bonds : bond 0.03309 ( 554) hydrogen bonds : angle 5.90599 ( 1419) link_ALPHA1-3 : bond 0.00916 ( 6) link_ALPHA1-3 : angle 1.69455 ( 18) link_ALPHA1-6 : bond 0.00373 ( 6) link_ALPHA1-6 : angle 2.07750 ( 18) link_BETA1-4 : bond 0.00352 ( 9) link_BETA1-4 : angle 3.17583 ( 27) link_NAG-ASN : bond 0.00826 ( 12) link_NAG-ASN : angle 4.67324 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9114 (mtp) cc_final: 0.8355 (mtm) REVERT: A 587 MET cc_start: 0.6540 (tmm) cc_final: 0.5828 (tmm) REVERT: A 597 TYR cc_start: 0.8923 (m-80) cc_final: 0.8509 (m-80) REVERT: A 620 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8636 (t0) REVERT: H 72 ASP cc_start: 0.8287 (t0) cc_final: 0.7908 (t0) REVERT: L 5 THR cc_start: 0.9056 (m) cc_final: 0.8832 (p) REVERT: L 105 GLU cc_start: 0.5668 (tm-30) cc_final: 0.5380 (tm-30) REVERT: B 286 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8637 (pt0) REVERT: I 53 ASP cc_start: 0.9019 (p0) cc_final: 0.8651 (p0) REVERT: I 55 ASN cc_start: 0.8997 (m-40) cc_final: 0.8532 (m-40) REVERT: I 72 ASP cc_start: 0.8171 (t0) cc_final: 0.7685 (t0) REVERT: I 85 ASP cc_start: 0.8830 (p0) cc_final: 0.8602 (p0) REVERT: I 89 MET cc_start: 0.8400 (tpp) cc_final: 0.7963 (tpp) REVERT: M 24 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8039 (ttm110) REVERT: M 39 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7752 (mtt90) REVERT: M 70 GLU cc_start: 0.8129 (tp30) cc_final: 0.7872 (tp30) REVERT: M 81 GLU cc_start: 0.8917 (pm20) cc_final: 0.8531 (pm20) REVERT: M 105 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8080 (mt-10) REVERT: C 601 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9219 (mm) REVERT: J 16 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8019 (mmt90) REVERT: J 82 MET cc_start: 0.8806 (mtt) cc_final: 0.8044 (mtm) outliers start: 48 outliers final: 33 residues processed: 225 average time/residue: 0.1624 time to fit residues: 53.6485 Evaluate side-chains 215 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 10.0000 chunk 217 optimal weight: 0.0060 chunk 124 optimal weight: 0.8980 chunk 198 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050894 restraints weight = 56129.560| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.06 r_work: 0.2767 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20388 Z= 0.102 Angle : 0.544 12.731 27774 Z= 0.264 Chirality : 0.043 0.281 3111 Planarity : 0.003 0.036 3531 Dihedral : 4.979 51.655 3402 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.29 % Allowed : 12.88 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2415 helix: 0.43 (0.29), residues: 342 sheet: -0.40 (0.17), residues: 861 loop : 0.02 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 328 TYR 0.026 0.001 TYR B 380 PHE 0.010 0.001 PHE A 508 TRP 0.007 0.001 TRP B 539 HIS 0.009 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00236 (20334) covalent geometry : angle 0.49825 (27633) SS BOND : bond 0.00443 ( 21) SS BOND : angle 2.24500 ( 42) hydrogen bonds : bond 0.03143 ( 554) hydrogen bonds : angle 5.75645 ( 1419) link_ALPHA1-3 : bond 0.00798 ( 6) link_ALPHA1-3 : angle 1.55819 ( 18) link_ALPHA1-6 : bond 0.00403 ( 6) link_ALPHA1-6 : angle 2.01386 ( 18) link_BETA1-4 : bond 0.00354 ( 9) link_BETA1-4 : angle 3.10645 ( 27) link_NAG-ASN : bond 0.00853 ( 12) link_NAG-ASN : angle 4.63763 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9126 (mtp) cc_final: 0.8402 (mtm) REVERT: A 587 MET cc_start: 0.6505 (tmm) cc_final: 0.5856 (tmm) REVERT: A 597 TYR cc_start: 0.8923 (m-80) cc_final: 0.8525 (m-80) REVERT: A 620 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8594 (t0) REVERT: H 13 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8359 (mmm160) REVERT: H 72 ASP cc_start: 0.8244 (t0) cc_final: 0.7977 (t0) REVERT: H 83 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7601 (ttp-110) REVERT: L 5 THR cc_start: 0.9076 (m) cc_final: 0.8868 (p) REVERT: L 105 GLU cc_start: 0.5833 (tm-30) cc_final: 0.5530 (tm-30) REVERT: I 53 ASP cc_start: 0.9035 (p0) cc_final: 0.8625 (p0) REVERT: I 55 ASN cc_start: 0.8990 (m-40) cc_final: 0.8547 (m110) REVERT: I 72 ASP cc_start: 0.8144 (t0) cc_final: 0.7674 (t0) REVERT: I 85 ASP cc_start: 0.8836 (p0) cc_final: 0.8598 (p0) REVERT: I 89 MET cc_start: 0.8397 (tpp) cc_final: 0.8065 (tpp) REVERT: M 39 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7831 (mtt90) REVERT: M 70 GLU cc_start: 0.8097 (tp30) cc_final: 0.7856 (tp30) REVERT: M 81 GLU cc_start: 0.8882 (pm20) cc_final: 0.8494 (pm20) REVERT: M 105 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8126 (mt-10) REVERT: C 601 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9196 (mm) REVERT: J 82 MET cc_start: 0.8845 (mtt) cc_final: 0.8028 (mtm) outliers start: 48 outliers final: 32 residues processed: 224 average time/residue: 0.1766 time to fit residues: 57.2988 Evaluate side-chains 212 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 214 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052059 restraints weight = 56250.186| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.07 r_work: 0.2746 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20388 Z= 0.138 Angle : 0.556 12.800 27774 Z= 0.269 Chirality : 0.043 0.289 3111 Planarity : 0.003 0.045 3531 Dihedral : 5.011 52.315 3402 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.00 % Allowed : 13.35 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2415 helix: 0.39 (0.29), residues: 342 sheet: -0.36 (0.17), residues: 861 loop : 0.05 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 178 TYR 0.025 0.001 TYR B 380 PHE 0.008 0.001 PHE A 508 TRP 0.006 0.001 TRP L 3 HIS 0.013 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00327 (20334) covalent geometry : angle 0.50998 (27633) SS BOND : bond 0.00323 ( 21) SS BOND : angle 2.35484 ( 42) hydrogen bonds : bond 0.03178 ( 554) hydrogen bonds : angle 5.70072 ( 1419) link_ALPHA1-3 : bond 0.00719 ( 6) link_ALPHA1-3 : angle 1.62050 ( 18) link_ALPHA1-6 : bond 0.00334 ( 6) link_ALPHA1-6 : angle 2.00765 ( 18) link_BETA1-4 : bond 0.00347 ( 9) link_BETA1-4 : angle 3.16291 ( 27) link_NAG-ASN : bond 0.00834 ( 12) link_NAG-ASN : angle 4.62503 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9119 (mtp) cc_final: 0.8398 (mtm) REVERT: A 587 MET cc_start: 0.6572 (tmm) cc_final: 0.5928 (tmm) REVERT: A 597 TYR cc_start: 0.8927 (m-80) cc_final: 0.8518 (m-80) REVERT: H 13 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8397 (mmm160) REVERT: H 72 ASP cc_start: 0.8242 (t0) cc_final: 0.8037 (t0) REVERT: H 83 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7610 (ttp-110) REVERT: L 5 THR cc_start: 0.9034 (m) cc_final: 0.8809 (p) REVERT: I 53 ASP cc_start: 0.9034 (p0) cc_final: 0.8613 (p0) REVERT: I 55 ASN cc_start: 0.9011 (m-40) cc_final: 0.8526 (m110) REVERT: I 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7649 (t0) REVERT: I 85 ASP cc_start: 0.8850 (p0) cc_final: 0.8613 (p0) REVERT: I 89 MET cc_start: 0.8373 (tpp) cc_final: 0.8030 (tpp) REVERT: M 39 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7814 (mtt90) REVERT: M 70 GLU cc_start: 0.8113 (tp30) cc_final: 0.7895 (tp30) REVERT: M 81 GLU cc_start: 0.8900 (pm20) cc_final: 0.8511 (pm20) REVERT: M 105 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 601 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9196 (mm) REVERT: N 76 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8560 (mmmt) REVERT: N 105 GLU cc_start: 0.6097 (tm-30) cc_final: 0.5470 (tm-30) outliers start: 42 outliers final: 34 residues processed: 216 average time/residue: 0.1694 time to fit residues: 53.0270 Evaluate side-chains 214 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN B 534 HIS B 620 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047963 restraints weight = 54743.309| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.87 r_work: 0.2682 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 20388 Z= 0.289 Angle : 0.658 12.858 27774 Z= 0.320 Chirality : 0.047 0.324 3111 Planarity : 0.004 0.047 3531 Dihedral : 5.710 53.845 3402 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.76 % Allowed : 13.40 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2415 helix: 0.64 (0.29), residues: 318 sheet: -0.38 (0.16), residues: 894 loop : -0.06 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 178 TYR 0.030 0.001 TYR B 380 PHE 0.018 0.002 PHE B 643 TRP 0.010 0.001 TRP I 47 HIS 0.011 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00676 (20334) covalent geometry : angle 0.61260 (27633) SS BOND : bond 0.00452 ( 21) SS BOND : angle 2.91371 ( 42) hydrogen bonds : bond 0.03832 ( 554) hydrogen bonds : angle 5.93391 ( 1419) link_ALPHA1-3 : bond 0.00491 ( 6) link_ALPHA1-3 : angle 2.07978 ( 18) link_ALPHA1-6 : bond 0.00601 ( 6) link_ALPHA1-6 : angle 2.20738 ( 18) link_BETA1-4 : bond 0.00752 ( 9) link_BETA1-4 : angle 3.57273 ( 27) link_NAG-ASN : bond 0.00844 ( 12) link_NAG-ASN : angle 4.66995 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9141 (mtp) cc_final: 0.8428 (mtm) REVERT: A 534 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (t-90) REVERT: A 587 MET cc_start: 0.6818 (tmm) cc_final: 0.6106 (tmm) REVERT: A 597 TYR cc_start: 0.8938 (m-80) cc_final: 0.8529 (m-80) REVERT: H 72 ASP cc_start: 0.8273 (t0) cc_final: 0.8032 (t0) REVERT: L 5 THR cc_start: 0.9049 (m) cc_final: 0.8727 (p) REVERT: L 77 ASN cc_start: 0.8095 (t0) cc_final: 0.7753 (t0) REVERT: I 53 ASP cc_start: 0.9032 (p0) cc_final: 0.8526 (p0) REVERT: I 55 ASN cc_start: 0.8957 (m-40) cc_final: 0.8439 (m110) REVERT: I 72 ASP cc_start: 0.8173 (t0) cc_final: 0.7714 (t0) REVERT: I 85 ASP cc_start: 0.8817 (p0) cc_final: 0.8586 (p0) REVERT: I 89 MET cc_start: 0.8362 (tpp) cc_final: 0.8001 (tpp) REVERT: M 24 ARG cc_start: 0.8373 (ttm110) cc_final: 0.7533 (mtp-110) REVERT: M 39 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7771 (mtt90) REVERT: M 81 GLU cc_start: 0.8934 (pm20) cc_final: 0.8512 (pm20) REVERT: M 105 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8187 (mt-10) REVERT: J 16 ARG cc_start: 0.8629 (ttm110) cc_final: 0.7955 (mmt90) REVERT: N 79 GLN cc_start: 0.8800 (mm110) cc_final: 0.8590 (mm110) REVERT: N 105 GLU cc_start: 0.6113 (tm-30) cc_final: 0.5388 (tm-30) outliers start: 37 outliers final: 30 residues processed: 210 average time/residue: 0.1801 time to fit residues: 55.4618 Evaluate side-chains 206 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 620 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051237 restraints weight = 56410.165| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.04 r_work: 0.2726 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20388 Z= 0.119 Angle : 0.574 12.723 27774 Z= 0.278 Chirality : 0.043 0.316 3111 Planarity : 0.003 0.041 3531 Dihedral : 5.326 51.283 3402 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.43 % Allowed : 14.07 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2415 helix: 0.46 (0.29), residues: 342 sheet: -0.38 (0.17), residues: 888 loop : -0.04 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 19 TYR 0.023 0.001 TYR B 380 PHE 0.012 0.001 PHE A 508 TRP 0.010 0.001 TRP C 354 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00278 (20334) covalent geometry : angle 0.53150 (27633) SS BOND : bond 0.00373 ( 21) SS BOND : angle 1.99326 ( 42) hydrogen bonds : bond 0.03332 ( 554) hydrogen bonds : angle 5.70201 ( 1419) link_ALPHA1-3 : bond 0.00809 ( 6) link_ALPHA1-3 : angle 1.61372 ( 18) link_ALPHA1-6 : bond 0.00295 ( 6) link_ALPHA1-6 : angle 1.92602 ( 18) link_BETA1-4 : bond 0.00321 ( 9) link_BETA1-4 : angle 3.12338 ( 27) link_NAG-ASN : bond 0.00816 ( 12) link_NAG-ASN : angle 4.70863 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.9030 (mtp) cc_final: 0.8315 (mtm) REVERT: A 534 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8237 (t-90) REVERT: A 587 MET cc_start: 0.6721 (tmm) cc_final: 0.5993 (tmm) REVERT: A 597 TYR cc_start: 0.8934 (m-80) cc_final: 0.8566 (m-80) REVERT: H 13 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8350 (mmm160) REVERT: H 72 ASP cc_start: 0.8289 (t0) cc_final: 0.8045 (t0) REVERT: L 5 THR cc_start: 0.8973 (m) cc_final: 0.8729 (p) REVERT: L 77 ASN cc_start: 0.8066 (t0) cc_final: 0.7741 (t0) REVERT: B 620 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8899 (t0) REVERT: I 53 ASP cc_start: 0.9037 (p0) cc_final: 0.8631 (p0) REVERT: I 55 ASN cc_start: 0.9006 (m-40) cc_final: 0.8509 (m110) REVERT: I 72 ASP cc_start: 0.8155 (t0) cc_final: 0.7653 (t0) REVERT: I 85 ASP cc_start: 0.8848 (p0) cc_final: 0.8619 (p0) REVERT: I 89 MET cc_start: 0.8305 (tpp) cc_final: 0.7935 (tpp) REVERT: M 39 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7795 (mtt90) REVERT: M 81 GLU cc_start: 0.8889 (pm20) cc_final: 0.8466 (pm20) REVERT: M 105 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 601 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9191 (mm) REVERT: J 82 MET cc_start: 0.8608 (mtt) cc_final: 0.8393 (mtm) REVERT: N 105 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5381 (tm-30) outliers start: 30 outliers final: 24 residues processed: 209 average time/residue: 0.1742 time to fit residues: 53.3577 Evaluate side-chains 201 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 21 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050976 restraints weight = 56561.894| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.03 r_work: 0.2722 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 20388 Z= 0.211 Angle : 0.733 59.200 27774 Z= 0.399 Chirality : 0.052 1.534 3111 Planarity : 0.003 0.061 3531 Dihedral : 5.321 51.296 3402 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.43 % Allowed : 14.07 % Favored : 84.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2415 helix: 0.46 (0.29), residues: 342 sheet: -0.37 (0.16), residues: 888 loop : -0.06 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 19 TYR 0.022 0.001 TYR B 380 PHE 0.040 0.001 PHE N 83 TRP 0.018 0.001 TRP I 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00450 (20334) covalent geometry : angle 0.70031 (27633) SS BOND : bond 0.00339 ( 21) SS BOND : angle 2.02721 ( 42) hydrogen bonds : bond 0.03368 ( 554) hydrogen bonds : angle 5.69656 ( 1419) link_ALPHA1-3 : bond 0.00848 ( 6) link_ALPHA1-3 : angle 1.60929 ( 18) link_ALPHA1-6 : bond 0.00427 ( 6) link_ALPHA1-6 : angle 2.00151 ( 18) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 3.16826 ( 27) link_NAG-ASN : bond 0.00814 ( 12) link_NAG-ASN : angle 4.70647 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.65 seconds wall clock time: 76 minutes 14.33 seconds (4574.33 seconds total)