Starting phenix.real_space_refine on Fri Sep 19 03:31:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d56_46575/09_2025/9d56_46575.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12262 atoms to isotropic. 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 52 5.16 5 C 7949 2.51 5 N 2017 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12440 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5976 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 702} Chain: "B" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6092 Classifications: {'peptide': 754} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 725} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "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: 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: "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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" 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: 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: "L" 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: "M" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.24, per 1000 atoms: 0.26 Number of scatterers: 12440 At special positions: 0 Unit cell: (140.17, 101.65, 128.4, 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 52 16.00 O 2422 8.00 N 2017 7.00 C 7949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 762 " distance=2.02 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 801 " - " ASN A 150 " " NAG A 802 " - " ASN A 92 " " NAG B 801 " - " ASN B 150 " " NAG C 1 " - " ASN A 229 " " NAG D 1 " - " ASN A 281 " " NAG E 1 " - " ASN A 219 " " NAG F 1 " - " ASN A 321 " " NAG G 1 " - " ASN A 85 " " NAG H 1 " - " ASN B 229 " " NAG I 1 " - " ASN B 281 " " NAG J 1 " - " ASN B 219 " " NAG K 1 " - " ASN B 321 " " NAG L 1 " - " ASN B 85 " " NAG M 1 " - " ASN B 92 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 599.8 milliseconds Enol-peptide restraints added in 1.4 microseconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 24 sheets defined 22.8% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 91 through 97 removed outlier: 4.132A pdb=" N PHE A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.572A pdb=" N ILE A 295 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.570A pdb=" N MET A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.573A pdb=" N TYR A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 600 through 615 Processing helix chain 'A' and resid 630 through 643 removed outlier: 4.155A pdb=" N GLY A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 687 through 698 removed outlier: 4.799A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.350A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 763 Processing helix chain 'B' and resid 18 through 36 Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.502A pdb=" N PHE B 95 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 497 through 507 removed outlier: 3.781A pdb=" N ASN B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 570 removed outlier: 3.614A pdb=" N TYR B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 600 through 615 Processing helix chain 'B' and resid 631 through 642 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 663 through 671 removed outlier: 3.666A pdb=" N TYR B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 687 through 690 Processing helix chain 'B' and resid 691 through 696 removed outlier: 3.886A pdb=" N LYS B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 4.048A pdb=" N SER B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 6.767A pdb=" N GLU A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 68 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 76 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.707A pdb=" N ASP A 104 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU A 115 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A 135 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU A 117 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP A 133 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN A 119 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 131 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 196 removed outlier: 4.407A pdb=" N PHE A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 305 removed outlier: 5.480A pdb=" N LEU A 300 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 305 removed outlier: 5.480A pdb=" N LEU A 300 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 411 removed outlier: 6.641A pdb=" N TYR A 416 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU A 410 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TYR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 457 through 461 Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 519 removed outlier: 3.763A pdb=" N LEU A 519 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 575 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A 576 " --> pdb=" O PRO A 541 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 543 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP A 545 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N TYR A 540 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 623 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP A 629 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS A 649 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 624 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N ILE A 651 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 626 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY A 628 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.846A pdb=" N ILE B 76 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 105 through 107 removed outlier: 4.807A pdb=" N TYR B 120 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 129 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 154 through 157 Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 196 removed outlier: 4.413A pdb=" N PHE B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AC1, first strand: chain 'B' and resid 298 through 305 removed outlier: 5.445A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 302 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 305 removed outlier: 5.445A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP B 302 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 410 removed outlier: 5.869A pdb=" N ILE B 407 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 418 " --> pdb=" O ILE B 407 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 454 through 461 removed outlier: 7.000A pdb=" N GLY B 474 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 457 " --> pdb=" O CYS B 472 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS B 472 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 459 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 470 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B 461 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR B 468 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 480 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL B 493 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 482 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 513 through 519 removed outlier: 3.738A pdb=" N VAL B 575 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B 578 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N TYR B 540 " --> pdb=" O ASN B 621 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG B 623 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 627 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N CYS B 649 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 624 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ILE B 651 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 626 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL B 653 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY B 628 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER B 630 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 705 " --> pdb=" O ALA B 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 704 " --> pdb=" O MET B 733 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 735 " --> pdb=" O HIS B 704 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1155 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: 2.49 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2421 1.33 - 1.45: 3513 1.45 - 1.57: 6770 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 12784 Sorted by residual: bond pdb=" C GLU B 604 " pdb=" N ASP B 605 " ideal model delta sigma weight residual 1.334 1.232 0.102 1.27e-02 6.20e+03 6.48e+01 bond pdb=" C ASP B 605 " pdb=" N GLN B 606 " ideal model delta sigma weight residual 1.335 1.436 -0.101 1.31e-02 5.83e+03 5.90e+01 bond pdb=" C THR B 152 " pdb=" N GLN B 153 " ideal model delta sigma weight residual 1.333 1.251 0.082 1.50e-02 4.44e+03 2.96e+01 bond pdb=" C ASN B 151 " pdb=" N THR B 152 " ideal model delta sigma weight residual 1.331 1.270 0.060 1.33e-02 5.65e+03 2.06e+01 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.457 1.493 -0.035 9.00e-03 1.23e+04 1.54e+01 ... (remaining 12779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12383 1.48 - 2.96: 4431 2.96 - 4.45: 540 4.45 - 5.93: 32 5.93 - 7.41: 5 Bond angle restraints: 17391 Sorted by residual: angle pdb=" CA GLU B 604 " pdb=" C GLU B 604 " pdb=" N ASP B 605 " ideal model delta sigma weight residual 117.07 124.48 -7.41 1.14e+00 7.69e-01 4.22e+01 angle pdb=" CA GLY A 587 " pdb=" C GLY A 587 " pdb=" O GLY A 587 " ideal model delta sigma weight residual 122.22 118.21 4.01 6.50e-01 2.37e+00 3.81e+01 angle pdb=" N TYR B 547 " pdb=" CA TYR B 547 " pdb=" C TYR B 547 " ideal model delta sigma weight residual 113.18 105.97 7.21 1.33e+00 5.65e-01 2.94e+01 angle pdb=" N GLN B 455 " pdb=" CA GLN B 455 " pdb=" C GLN B 455 " ideal model delta sigma weight residual 114.56 107.72 6.84 1.27e+00 6.20e-01 2.90e+01 angle pdb=" CA GLY B 355 " pdb=" C GLY B 355 " pdb=" O GLY B 355 " ideal model delta sigma weight residual 122.29 118.10 4.19 8.10e-01 1.52e+00 2.68e+01 ... (remaining 17386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 7155 21.02 - 42.05: 527 42.05 - 63.07: 99 63.07 - 84.09: 24 84.09 - 105.12: 8 Dihedral angle restraints: 7813 sinusoidal: 3415 harmonic: 4398 Sorted by residual: dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CD ARG A 336 " pdb=" NE ARG A 336 " pdb=" CZ ARG A 336 " pdb=" NH1 ARG A 336 " ideal model delta sinusoidal sigma weight residual 0.00 -77.33 77.33 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 385 " pdb=" SG CYS B 385 " pdb=" SG CYS B 394 " pdb=" CB CYS B 394 " ideal model delta sinusoidal sigma weight residual 93.00 163.03 -70.03 1 1.00e+01 1.00e-02 6.32e+01 ... (remaining 7810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1066 0.089 - 0.177: 738 0.177 - 0.265: 111 0.265 - 0.354: 3 0.354 - 0.442: 2 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 1917 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 336 " 1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 336 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 336 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 336 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 336 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 801 " 0.120 2.00e-02 2.50e+03 9.94e-02 1.23e+02 pdb=" C7 NAG B 801 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG B 801 " 0.090 2.00e-02 2.50e+03 pdb=" N2 NAG B 801 " -0.159 2.00e-02 2.50e+03 pdb=" O7 NAG B 801 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 54 " 0.884 9.50e-02 1.11e+02 3.96e-01 9.52e+01 pdb=" NE ARG A 54 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 54 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 54 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 54 " 0.023 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5468 2.91 - 3.41: 11786 3.41 - 3.90: 23700 3.90 - 4.40: 26481 4.40 - 4.90: 41797 Nonbonded interactions: 109232 Sorted by model distance: nonbonded pdb=" O PRO A 149 " pdb=" OG1 THR A 152 " model vdw 2.409 3.040 nonbonded pdb=" O LEU A 519 " pdb=" OG1 THR A 522 " model vdw 2.421 3.040 nonbonded pdb=" O LEU B 519 " pdb=" OG1 THR B 522 " model vdw 2.425 3.040 nonbonded pdb=" O THR A 411 " pdb=" N ASP A 413 " model vdw 2.431 3.120 nonbonded pdb=" O GLY A 672 " pdb=" OH TYR A 683 " model vdw 2.436 3.040 ... (remaining 109227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 801)) selection = (chain 'B' and resid 37 through 801) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.012 0.102 12817 Z= 0.936 Angle : 1.385 7.409 17484 Z= 1.064 Chirality : 0.101 0.442 1920 Planarity : 0.025 0.482 2178 Dihedral : 14.996 105.115 4991 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.80 % Favored : 94.80 % Rotamer: Outliers : 3.44 % Allowed : 7.42 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -1.46 (0.20), residues: 1480 helix: -0.15 (0.29), residues: 250 sheet: -0.79 (0.23), residues: 439 loop : -1.31 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 611 TYR 0.016 0.002 TYR B 68 PHE 0.022 0.002 PHE A 387 TRP 0.017 0.002 TRP A 627 HIS 0.007 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.01229 (12784) covalent geometry : angle 1.38537 (17391) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.36403 ( 12) hydrogen bonds : bond 0.19570 ( 418) hydrogen bonds : angle 8.26509 ( 1155) link_BETA1-4 : bond 0.00216 ( 13) link_BETA1-4 : angle 1.05896 ( 39) link_NAG-ASN : bond 0.00486 ( 14) link_NAG-ASN : angle 1.66522 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8711 (m) REVERT: A 346 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8903 (mt) REVERT: A 591 MET cc_start: 0.8097 (ttp) cc_final: 0.7845 (ttt) outliers start: 45 outliers final: 8 residues processed: 146 average time/residue: 0.1538 time to fit residues: 30.6930 Evaluate side-chains 68 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 170 ASN A 263 ASN A 435 GLN A 533 HIS A 731 GLN A 754 HIS B 138 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 314 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 HIS ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062355 restraints weight = 61886.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063826 restraints weight = 27805.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.064736 restraints weight = 15634.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065330 restraints weight = 10142.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.065745 restraints weight = 7232.964| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12817 Z= 0.133 Angle : 0.575 7.290 17484 Z= 0.308 Chirality : 0.043 0.298 1920 Planarity : 0.004 0.052 2178 Dihedral : 7.444 63.650 2235 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.76 % Allowed : 10.63 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.84 (0.20), residues: 1480 helix: 0.78 (0.32), residues: 268 sheet: -0.49 (0.22), residues: 475 loop : -1.06 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 54 TYR 0.018 0.001 TYR A 700 PHE 0.022 0.002 PHE A 387 TRP 0.012 0.001 TRP B 216 HIS 0.012 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00271 (12784) covalent geometry : angle 0.56548 (17391) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.91394 ( 12) hydrogen bonds : bond 0.04406 ( 418) hydrogen bonds : angle 5.96271 ( 1155) link_BETA1-4 : bond 0.00414 ( 13) link_BETA1-4 : angle 1.50417 ( 39) link_NAG-ASN : bond 0.00280 ( 14) link_NAG-ASN : angle 1.65125 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8511 (ttpt) REVERT: A 141 GLN cc_start: 0.7670 (tt0) cc_final: 0.7361 (tt0) REVERT: A 266 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8728 (m) REVERT: A 671 MET cc_start: 0.8612 (tpt) cc_final: 0.8275 (tpt) REVERT: A 699 GLU cc_start: 0.7488 (mp0) cc_final: 0.7267 (mp0) REVERT: B 509 MET cc_start: 0.7524 (mmm) cc_final: 0.7281 (mmm) REVERT: B 733 MET cc_start: 0.7566 (tpp) cc_final: 0.7104 (tpp) outliers start: 23 outliers final: 12 residues processed: 80 average time/residue: 0.1505 time to fit residues: 16.7629 Evaluate side-chains 62 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 chunk 61 optimal weight: 0.0030 chunk 23 optimal weight: 0.0870 chunk 75 optimal weight: 9.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS B 435 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061863 restraints weight = 62264.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063350 restraints weight = 27884.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064286 restraints weight = 15701.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064874 restraints weight = 10086.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065297 restraints weight = 7218.769| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12817 Z= 0.095 Angle : 0.491 7.354 17484 Z= 0.263 Chirality : 0.042 0.204 1920 Planarity : 0.004 0.035 2178 Dihedral : 5.902 58.447 2231 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.92 % Allowed : 11.31 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.66 (0.21), residues: 1480 helix: 0.86 (0.32), residues: 262 sheet: -0.36 (0.22), residues: 470 loop : -0.90 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 147 TYR 0.010 0.001 TYR A 752 PHE 0.019 0.001 PHE A 387 TRP 0.012 0.001 TRP A 627 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00200 (12784) covalent geometry : angle 0.48251 (17391) SS BOND : bond 0.00513 ( 6) SS BOND : angle 0.92937 ( 12) hydrogen bonds : bond 0.03721 ( 418) hydrogen bonds : angle 5.43250 ( 1155) link_BETA1-4 : bond 0.00447 ( 13) link_BETA1-4 : angle 1.32648 ( 39) link_NAG-ASN : bond 0.00220 ( 14) link_NAG-ASN : angle 1.40912 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8546 (ttpt) REVERT: A 141 GLN cc_start: 0.7743 (tt0) cc_final: 0.7462 (tt0) REVERT: A 266 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8764 (m) REVERT: A 638 MET cc_start: 0.9027 (mmp) cc_final: 0.8635 (mmm) REVERT: A 671 MET cc_start: 0.8628 (tpt) cc_final: 0.8264 (tpt) REVERT: A 699 GLU cc_start: 0.7504 (mp0) cc_final: 0.7253 (mp0) REVERT: B 509 MET cc_start: 0.7555 (mmm) cc_final: 0.7338 (mmm) REVERT: B 733 MET cc_start: 0.7758 (tpp) cc_final: 0.7042 (tpp) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.1546 time to fit residues: 13.7950 Evaluate side-chains 60 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 202 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 overall best weight: 1.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 153 GLN B 170 ASN B 506 ASN B 508 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058671 restraints weight = 61818.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060072 restraints weight = 28120.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.060974 restraints weight = 16125.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061567 restraints weight = 10571.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061983 restraints weight = 7621.023| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12817 Z= 0.165 Angle : 0.524 8.047 17484 Z= 0.277 Chirality : 0.042 0.185 1920 Planarity : 0.003 0.033 2178 Dihedral : 5.546 58.816 2228 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.83 % Allowed : 11.31 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.57 (0.21), residues: 1480 helix: 1.05 (0.33), residues: 250 sheet: -0.39 (0.22), residues: 468 loop : -0.80 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 318 TYR 0.014 0.001 TYR A 299 PHE 0.022 0.002 PHE A 387 TRP 0.010 0.001 TRP B 216 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00356 (12784) covalent geometry : angle 0.51491 (17391) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.02630 ( 12) hydrogen bonds : bond 0.03703 ( 418) hydrogen bonds : angle 5.21936 ( 1155) link_BETA1-4 : bond 0.00406 ( 13) link_BETA1-4 : angle 1.48279 ( 39) link_NAG-ASN : bond 0.00266 ( 14) link_NAG-ASN : angle 1.54089 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8477 (ttpt) REVERT: A 141 GLN cc_start: 0.7799 (tt0) cc_final: 0.7538 (tt0) REVERT: A 266 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 638 MET cc_start: 0.9043 (mmp) cc_final: 0.8629 (mmm) REVERT: A 671 MET cc_start: 0.8737 (tpt) cc_final: 0.8339 (tpt) REVERT: A 699 GLU cc_start: 0.7577 (mp0) cc_final: 0.7256 (mp0) REVERT: B 733 MET cc_start: 0.7963 (tpp) cc_final: 0.6983 (tpp) outliers start: 24 outliers final: 8 residues processed: 77 average time/residue: 0.1386 time to fit residues: 15.2351 Evaluate side-chains 62 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.059192 restraints weight = 61849.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060601 restraints weight = 27869.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061493 restraints weight = 15991.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062087 restraints weight = 10553.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062524 restraints weight = 7625.532| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12817 Z= 0.102 Angle : 0.476 8.540 17484 Z= 0.253 Chirality : 0.041 0.191 1920 Planarity : 0.003 0.033 2178 Dihedral : 5.303 55.775 2226 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.15 % Allowed : 11.77 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.50 (0.21), residues: 1480 helix: 0.97 (0.32), residues: 251 sheet: -0.31 (0.22), residues: 471 loop : -0.73 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 684 TYR 0.026 0.001 TYR A 118 PHE 0.020 0.001 PHE A 387 TRP 0.009 0.001 TRP A 315 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00217 (12784) covalent geometry : angle 0.46737 (17391) SS BOND : bond 0.00271 ( 6) SS BOND : angle 1.35590 ( 12) hydrogen bonds : bond 0.03339 ( 418) hydrogen bonds : angle 5.10847 ( 1155) link_BETA1-4 : bond 0.00357 ( 13) link_BETA1-4 : angle 1.27221 ( 39) link_NAG-ASN : bond 0.00182 ( 14) link_NAG-ASN : angle 1.36328 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8867 (ptpt) cc_final: 0.8436 (ttpt) REVERT: A 141 GLN cc_start: 0.7769 (tt0) cc_final: 0.7561 (tt0) REVERT: A 266 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8780 (m) REVERT: A 671 MET cc_start: 0.8684 (tpt) cc_final: 0.8256 (tpt) REVERT: A 699 GLU cc_start: 0.7512 (mp0) cc_final: 0.7186 (mp0) REVERT: B 98 PHE cc_start: 0.6835 (t80) cc_final: 0.6609 (t80) REVERT: B 733 MET cc_start: 0.8006 (tpp) cc_final: 0.6901 (tpp) outliers start: 15 outliers final: 7 residues processed: 66 average time/residue: 0.1199 time to fit residues: 11.7873 Evaluate side-chains 61 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 508 GLN B 694 ASN ** B 712 HIS ** 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 = 0.3304 r_free = 0.3304 target = 0.060706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055030 restraints weight = 64123.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056405 restraints weight = 29438.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.057268 restraints weight = 17149.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057869 restraints weight = 11504.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.058285 restraints weight = 8382.544| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12817 Z= 0.282 Angle : 0.622 8.753 17484 Z= 0.327 Chirality : 0.045 0.171 1920 Planarity : 0.004 0.035 2178 Dihedral : 5.934 54.281 2226 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.53 % Allowed : 11.85 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.68 (0.21), residues: 1480 helix: 0.72 (0.33), residues: 252 sheet: -0.47 (0.22), residues: 468 loop : -0.76 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 253 TYR 0.025 0.002 TYR B 526 PHE 0.026 0.002 PHE A 758 TRP 0.016 0.002 TRP B 216 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00617 (12784) covalent geometry : angle 0.61105 (17391) SS BOND : bond 0.00227 ( 6) SS BOND : angle 1.10535 ( 12) hydrogen bonds : bond 0.04189 ( 418) hydrogen bonds : angle 5.37182 ( 1155) link_BETA1-4 : bond 0.00398 ( 13) link_BETA1-4 : angle 1.59293 ( 39) link_NAG-ASN : bond 0.00578 ( 14) link_NAG-ASN : angle 1.88949 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8749 (mmtt) REVERT: A 112 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: A 266 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.8816 (m) REVERT: A 671 MET cc_start: 0.8701 (tpt) cc_final: 0.8170 (tpt) REVERT: A 699 GLU cc_start: 0.7595 (mp0) cc_final: 0.7196 (mp0) REVERT: B 733 MET cc_start: 0.8287 (tpp) cc_final: 0.6962 (tpp) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.1332 time to fit residues: 13.3796 Evaluate side-chains 60 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 91 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 508 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056843 restraints weight = 62875.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058244 restraints weight = 28792.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059115 restraints weight = 16639.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059710 restraints weight = 11024.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060139 restraints weight = 7999.690| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12817 Z= 0.128 Angle : 0.509 9.650 17484 Z= 0.270 Chirality : 0.043 0.187 1920 Planarity : 0.003 0.032 2178 Dihedral : 5.611 52.874 2226 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.92 % Allowed : 12.61 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.57 (0.21), residues: 1480 helix: 0.82 (0.33), residues: 252 sheet: -0.35 (0.23), residues: 467 loop : -0.74 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 140 TYR 0.020 0.001 TYR A 118 PHE 0.018 0.001 PHE A 387 TRP 0.012 0.001 TRP A 315 HIS 0.005 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00279 (12784) covalent geometry : angle 0.50141 (17391) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.86505 ( 12) hydrogen bonds : bond 0.03458 ( 418) hydrogen bonds : angle 5.09846 ( 1155) link_BETA1-4 : bond 0.00324 ( 13) link_BETA1-4 : angle 1.33236 ( 39) link_NAG-ASN : bond 0.00199 ( 14) link_NAG-ASN : angle 1.42684 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8603 (pttt) REVERT: A 266 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8773 (m) REVERT: A 671 MET cc_start: 0.8654 (tpt) cc_final: 0.8153 (tpt) REVERT: B 98 PHE cc_start: 0.6938 (t80) cc_final: 0.6663 (t80) REVERT: B 733 MET cc_start: 0.8242 (tpp) cc_final: 0.6779 (tpp) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.1244 time to fit residues: 11.5784 Evaluate side-chains 56 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 508 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057146 restraints weight = 62552.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058537 restraints weight = 28676.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059418 restraints weight = 16613.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060003 restraints weight = 10966.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060438 restraints weight = 7963.474| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12817 Z= 0.112 Angle : 0.501 9.894 17484 Z= 0.264 Chirality : 0.042 0.183 1920 Planarity : 0.003 0.033 2178 Dihedral : 5.549 53.314 2226 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.92 % Allowed : 13.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.51 (0.21), residues: 1480 helix: 0.89 (0.32), residues: 253 sheet: -0.29 (0.23), residues: 465 loop : -0.73 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 184 TYR 0.019 0.001 TYR A 118 PHE 0.018 0.001 PHE A 387 TRP 0.016 0.001 TRP A 187 HIS 0.005 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00241 (12784) covalent geometry : angle 0.49244 (17391) SS BOND : bond 0.00151 ( 6) SS BOND : angle 0.80380 ( 12) hydrogen bonds : bond 0.03333 ( 418) hydrogen bonds : angle 5.02420 ( 1155) link_BETA1-4 : bond 0.00327 ( 13) link_BETA1-4 : angle 1.33376 ( 39) link_NAG-ASN : bond 0.00195 ( 14) link_NAG-ASN : angle 1.42776 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7133 (t0) REVERT: A 246 LEU cc_start: 0.8949 (tp) cc_final: 0.8713 (tp) REVERT: A 266 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8765 (m) REVERT: A 671 MET cc_start: 0.8686 (tpt) cc_final: 0.8194 (tpt) REVERT: B 733 MET cc_start: 0.8252 (tpp) cc_final: 0.6735 (tpp) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.1188 time to fit residues: 10.2851 Evaluate side-chains 55 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 313 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 107 optimal weight: 0.0370 chunk 73 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056606 restraints weight = 62877.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057995 restraints weight = 28878.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058887 restraints weight = 16779.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059445 restraints weight = 11084.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059854 restraints weight = 8100.712| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12817 Z= 0.141 Angle : 0.511 9.249 17484 Z= 0.269 Chirality : 0.042 0.179 1920 Planarity : 0.003 0.032 2178 Dihedral : 5.530 52.826 2224 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.15 % Allowed : 12.61 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.53 (0.21), residues: 1480 helix: 0.79 (0.32), residues: 259 sheet: -0.30 (0.23), residues: 465 loop : -0.72 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 184 TYR 0.018 0.001 TYR A 118 PHE 0.018 0.001 PHE A 387 TRP 0.011 0.001 TRP A 187 HIS 0.005 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00308 (12784) covalent geometry : angle 0.50275 (17391) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.82922 ( 12) hydrogen bonds : bond 0.03369 ( 418) hydrogen bonds : angle 4.99807 ( 1155) link_BETA1-4 : bond 0.00308 ( 13) link_BETA1-4 : angle 1.35803 ( 39) link_NAG-ASN : bond 0.00230 ( 14) link_NAG-ASN : angle 1.49962 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: A 139 LYS cc_start: 0.9058 (pttt) cc_final: 0.8293 (pttp) REVERT: A 171 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7096 (t0) REVERT: A 638 MET cc_start: 0.9017 (mmm) cc_final: 0.8675 (mmm) REVERT: A 671 MET cc_start: 0.8690 (tpt) cc_final: 0.8236 (tpt) REVERT: B 733 MET cc_start: 0.8277 (tpp) cc_final: 0.6738 (tpp) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 0.1208 time to fit residues: 11.0883 Evaluate side-chains 58 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 508 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.062946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.057301 restraints weight = 62855.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058696 restraints weight = 28809.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059600 restraints weight = 16683.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.060187 restraints weight = 10941.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060633 restraints weight = 7894.723| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12817 Z= 0.101 Angle : 0.510 9.834 17484 Z= 0.268 Chirality : 0.042 0.185 1920 Planarity : 0.003 0.032 2178 Dihedral : 5.456 53.326 2223 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.07 % Allowed : 12.92 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.49 (0.21), residues: 1480 helix: 0.83 (0.32), residues: 260 sheet: -0.26 (0.23), residues: 464 loop : -0.71 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.019 0.001 TYR A 118 PHE 0.016 0.001 PHE A 387 TRP 0.012 0.001 TRP B 157 HIS 0.006 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00219 (12784) covalent geometry : angle 0.50289 (17391) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.78229 ( 12) hydrogen bonds : bond 0.03222 ( 418) hydrogen bonds : angle 4.92694 ( 1155) link_BETA1-4 : bond 0.00316 ( 13) link_BETA1-4 : angle 1.29133 ( 39) link_NAG-ASN : bond 0.00194 ( 14) link_NAG-ASN : angle 1.39268 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: A 171 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7032 (t0) REVERT: A 638 MET cc_start: 0.9000 (mmm) cc_final: 0.8662 (mmm) REVERT: A 671 MET cc_start: 0.8679 (tpt) cc_final: 0.8227 (tpt) REVERT: A 755 MET cc_start: 0.7660 (mtm) cc_final: 0.7039 (mtm) REVERT: B 733 MET cc_start: 0.8245 (tpp) cc_final: 0.6689 (tpp) outliers start: 14 outliers final: 10 residues processed: 61 average time/residue: 0.1271 time to fit residues: 11.6036 Evaluate side-chains 60 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 chunk 29 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 overall best weight: 2.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.060624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054958 restraints weight = 63161.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056360 restraints weight = 29315.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057237 restraints weight = 16956.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057798 restraints weight = 11282.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058249 restraints weight = 8280.119| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12817 Z= 0.229 Angle : 0.597 9.997 17484 Z= 0.310 Chirality : 0.044 0.165 1920 Planarity : 0.004 0.047 2178 Dihedral : 5.832 53.702 2223 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.15 % Allowed : 12.92 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 aren not related in a simple way. whole: -0.63 (0.21), residues: 1480 helix: 0.68 (0.32), residues: 260 sheet: -0.41 (0.23), residues: 468 loop : -0.74 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 253 TYR 0.018 0.002 TYR B 120 PHE 0.020 0.002 PHE A 758 TRP 0.013 0.002 TRP B 215 HIS 0.005 0.001 HIS B 748 Details of bonding type rmsd covalent geometry : bond 0.00506 (12784) covalent geometry : angle 0.58752 (17391) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.96071 ( 12) hydrogen bonds : bond 0.03768 ( 418) hydrogen bonds : angle 5.10637 ( 1155) link_BETA1-4 : bond 0.00335 ( 13) link_BETA1-4 : angle 1.51423 ( 39) link_NAG-ASN : bond 0.00401 ( 14) link_NAG-ASN : angle 1.71059 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.40 seconds wall clock time: 34 minutes 41.37 seconds (2081.37 seconds total)