Starting phenix.real_space_refine on Wed Mar 4 15:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opn_20150/03_2026/6opn_20150.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 8949 2.51 5 N 2418 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14241 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2753 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 6 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'N07': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, G, E, H, F, I, L, N, M, O Time building chain proxies: 2.89, per 1000 atoms: 0.20 Number of scatterers: 14241 At special positions: 0 Unit cell: (147.29, 150.38, 111.24, 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 90 16.00 O 2784 8.00 N 2418 7.00 C 8949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.21 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.21 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.21 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 362 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 413 " " NAG A 616 " - " ASN A 448 " " NAG D 601 " - " ASN D 234 " " NAG D 609 " - " ASN D 276 " " NAG D 610 " - " ASN D 295 " " NAG D 611 " - " ASN D 332 " " NAG D 612 " - " ASN D 362 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 615 " - " ASN D 413 " " NAG D 616 " - " ASN D 448 " " NAG G 601 " - " ASN G 234 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 295 " " NAG G 611 " - " ASN G 332 " " NAG G 612 " - " ASN G 362 " " NAG G 613 " - " ASN G 386 " " NAG G 614 " - " ASN G 392 " " NAG G 615 " - " ASN G 413 " " NAG G 616 " - " ASN G 448 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN D 241 " " NAG M 1 " - " ASN D 262 " " NAG N 1 " - " ASN G 241 " " NAG O 1 " - " ASN G 262 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 558.1 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 31.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.891A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.907A pdb=" N ASN A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.979A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 547 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.891A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.906A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.978A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 547 Processing helix chain 'E' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 659 Processing helix chain 'F' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.892A pdb=" N HIS G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.906A pdb=" N ASN G 98 " --> pdb=" O MET G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.817A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.979A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 547 Processing helix chain 'H' and resid 569 through 593 removed outlier: 3.650A pdb=" N ARG H 579 " --> pdb=" O GLN H 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 597 Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 626 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 659 Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.024A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.533A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.431A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 91 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 202 Processing sheet with id=AB6, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.534A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.431A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 284 through 298 current: chain 'D' and resid 358 through 361 Processing sheet with id=AB7, first strand: chain 'D' and resid 271 through 273 removed outlier: 10.431A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 443 through 456 current: chain 'D' and resid 413 through 420 Processing sheet with id=AB8, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 91 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS F 35 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 12 through 17 Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC5, first strand: chain 'G' and resid 199 through 202 Processing sheet with id=AC6, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.532A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 358 through 361 Processing sheet with id=AC7, first strand: chain 'G' and resid 271 through 273 removed outlier: 10.432A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 420 Processing sheet with id=AC8, first strand: chain 'I' and resid 2 through 3 removed outlier: 6.799A pdb=" N LYS I 2 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 91 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS I 35 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 12 through 17 600 hydrogen bonds defined for protein. 1557 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: 2.35 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3296 1.32 - 1.45: 3933 1.45 - 1.58: 7125 1.58 - 1.71: 31 1.71 - 1.84: 117 Bond restraints: 14502 Sorted by residual: bond pdb=" C1 NAG D 601 " pdb=" O5 NAG D 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 NAG A 615 " pdb=" O5 NAG A 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG D 615 " pdb=" O5 NAG D 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 14497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 18185 3.17 - 6.34: 1312 6.34 - 9.50: 135 9.50 - 12.67: 12 12.67 - 15.84: 3 Bond angle restraints: 19647 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 120.03 128.18 -8.15 9.90e-01 1.02e+00 6.78e+01 angle pdb=" C PRO G 437 " pdb=" N PRO G 438 " pdb=" CA PRO G 438 " ideal model delta sigma weight residual 120.03 128.17 -8.14 9.90e-01 1.02e+00 6.75e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 120.03 128.15 -8.12 9.90e-01 1.02e+00 6.73e+01 angle pdb=" C ALA G 436 " pdb=" N PRO G 437 " pdb=" CA PRO G 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.88e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.26 -7.88 1.03e+00 9.43e-01 5.85e+01 ... (remaining 19642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 9024 22.20 - 44.39: 252 44.39 - 66.59: 66 66.59 - 88.78: 30 88.78 - 110.98: 12 Dihedral angle restraints: 9384 sinusoidal: 4464 harmonic: 4920 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.87 85.87 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.86 85.86 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.85 85.85 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 9381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1732 0.110 - 0.220: 554 0.220 - 0.330: 60 0.330 - 0.440: 9 0.440 - 0.550: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.60e+01 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.52e+01 ... (remaining 2355 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 332 " -0.060 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" CG ASN G 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN G 332 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN G 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG G 611 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.062 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN D 392 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG D 614 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.060 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN A 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG A 611 " -0.079 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4100 2.81 - 3.34: 12993 3.34 - 3.86: 23772 3.86 - 4.38: 27907 4.38 - 4.90: 45125 Nonbonded interactions: 113897 Sorted by model distance: nonbonded pdb=" OG1 THR D 373 " pdb=" O CYS D 385 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR G 373 " pdb=" O CYS G 385 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 373 " pdb=" O CYS A 385 " model vdw 2.295 3.040 nonbonded pdb=" O4 NAG D 614 " pdb=" O6 NAG D 614 " model vdw 2.391 3.040 nonbonded pdb=" O4 NAG G 614 " pdb=" O6 NAG G 614 " model vdw 2.391 3.040 ... (remaining 113892 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.022 0.184 14580 Z= 1.164 Angle : 1.806 15.840 19851 Z= 1.153 Chirality : 0.103 0.550 2358 Planarity : 0.009 0.057 2427 Dihedral : 12.345 110.976 6090 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1653 helix: 0.40 (0.22), residues: 405 sheet: 1.27 (0.24), residues: 381 loop : 0.08 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 469 TYR 0.028 0.006 TYR D 484 PHE 0.029 0.007 PHE A 353 TRP 0.053 0.010 TRP C 28 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.02168 (14502) covalent geometry : angle 1.78131 (19647) SS BOND : bond 0.05837 ( 30) SS BOND : angle 2.72245 ( 60) hydrogen bonds : bond 0.19013 ( 576) hydrogen bonds : angle 7.34093 ( 1557) link_ALPHA1-2 : bond 0.04481 ( 3) link_ALPHA1-2 : angle 3.35222 ( 9) link_ALPHA1-3 : bond 0.03369 ( 3) link_ALPHA1-3 : angle 2.19136 ( 9) link_BETA1-4 : bond 0.03345 ( 9) link_BETA1-4 : angle 4.90453 ( 27) link_NAG-ASN : bond 0.03369 ( 33) link_NAG-ASN : angle 3.43507 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7717 (ttm) cc_final: 0.7513 (ttm) REVERT: B 530 MET cc_start: 0.7404 (mtm) cc_final: 0.6762 (mtp) REVERT: D 275 GLU cc_start: 0.7020 (tt0) cc_final: 0.6259 (tt0) REVERT: D 371 ILE cc_start: 0.8266 (pt) cc_final: 0.7818 (pt) REVERT: E 530 MET cc_start: 0.7434 (mtm) cc_final: 0.6819 (mtp) REVERT: F 1 LYS cc_start: 0.7755 (pttm) cc_final: 0.7502 (pttp) REVERT: G 371 ILE cc_start: 0.8274 (pt) cc_final: 0.7772 (pt) REVERT: H 530 MET cc_start: 0.7459 (mtm) cc_final: 0.6891 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1316 time to fit residues: 76.1564 Evaluate side-chains 184 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN F 40 GLN I 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.103458 restraints weight = 43413.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.107004 restraints weight = 22465.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.109428 restraints weight = 13966.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.111097 restraints weight = 9699.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.112249 restraints weight = 7300.765| |-----------------------------------------------------------------------------| r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14580 Z= 0.219 Angle : 0.897 9.459 19851 Z= 0.457 Chirality : 0.050 0.184 2358 Planarity : 0.005 0.059 2427 Dihedral : 9.149 63.369 2805 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.56 % Allowed : 9.37 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1653 helix: 1.28 (0.26), residues: 405 sheet: 0.09 (0.24), residues: 348 loop : -0.23 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 252 TYR 0.018 0.003 TYR D 486 PHE 0.020 0.003 PHE G 383 TRP 0.025 0.003 TRP G 96 HIS 0.008 0.002 HIS E 641 Details of bonding type rmsd covalent geometry : bond 0.00481 (14502) covalent geometry : angle 0.86024 (19647) SS BOND : bond 0.00555 ( 30) SS BOND : angle 1.66448 ( 60) hydrogen bonds : bond 0.06873 ( 576) hydrogen bonds : angle 5.66426 ( 1557) link_ALPHA1-2 : bond 0.00145 ( 3) link_ALPHA1-2 : angle 1.84767 ( 9) link_ALPHA1-3 : bond 0.00769 ( 3) link_ALPHA1-3 : angle 2.62237 ( 9) link_BETA1-4 : bond 0.00313 ( 9) link_BETA1-4 : angle 4.17027 ( 27) link_NAG-ASN : bond 0.00307 ( 33) link_NAG-ASN : angle 2.69513 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6632 (mm-30) REVERT: C 1 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7055 (pptt) REVERT: C 51 LEU cc_start: 0.8120 (mm) cc_final: 0.7823 (mp) REVERT: C 73 ASN cc_start: 0.9219 (t0) cc_final: 0.8981 (t0) REVERT: D 69 TRP cc_start: 0.8016 (t60) cc_final: 0.7430 (t-100) REVERT: D 373 THR cc_start: 0.7799 (t) cc_final: 0.7496 (t) REVERT: D 482 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6854 (tp30) REVERT: E 530 MET cc_start: 0.7617 (mtm) cc_final: 0.7383 (mtp) REVERT: E 592 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6579 (mt) REVERT: G 69 TRP cc_start: 0.8038 (t60) cc_final: 0.7710 (t-100) REVERT: G 217 TYR cc_start: 0.6197 (m-80) cc_final: 0.5807 (m-80) REVERT: G 373 THR cc_start: 0.7851 (t) cc_final: 0.7521 (t) REVERT: G 482 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6701 (mm-30) REVERT: H 530 MET cc_start: 0.7558 (mtm) cc_final: 0.7100 (mtm) REVERT: H 592 LEU cc_start: 0.8252 (mt) cc_final: 0.7347 (mt) REVERT: I 1 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6788 (pptt) REVERT: I 73 ASN cc_start: 0.9209 (t0) cc_final: 0.8977 (t0) REVERT: I 92 GLU cc_start: 0.8250 (pm20) cc_final: 0.8025 (mp0) outliers start: 54 outliers final: 26 residues processed: 272 average time/residue: 0.1225 time to fit residues: 48.3935 Evaluate side-chains 196 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain C residue 1 LYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 652 GLN C 25 GLN D 229 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN I 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.121549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.104446 restraints weight = 43529.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.108049 restraints weight = 22298.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.110506 restraints weight = 13785.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.112150 restraints weight = 9537.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.113387 restraints weight = 7173.713| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14580 Z= 0.147 Angle : 0.737 8.619 19851 Z= 0.372 Chirality : 0.045 0.156 2358 Planarity : 0.004 0.048 2427 Dihedral : 7.937 59.065 2805 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.70 % Allowed : 10.63 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1653 helix: 1.55 (0.26), residues: 405 sheet: -0.19 (0.26), residues: 318 loop : -0.38 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 54 TYR 0.015 0.002 TYR D 486 PHE 0.018 0.002 PHE B 522 TRP 0.040 0.002 TRP F 28 HIS 0.005 0.001 HIS H 641 Details of bonding type rmsd covalent geometry : bond 0.00321 (14502) covalent geometry : angle 0.70817 (19647) SS BOND : bond 0.00517 ( 30) SS BOND : angle 1.56668 ( 60) hydrogen bonds : bond 0.05426 ( 576) hydrogen bonds : angle 5.17048 ( 1557) link_ALPHA1-2 : bond 0.00155 ( 3) link_ALPHA1-2 : angle 1.66216 ( 9) link_ALPHA1-3 : bond 0.01107 ( 3) link_ALPHA1-3 : angle 1.35367 ( 9) link_BETA1-4 : bond 0.00409 ( 9) link_BETA1-4 : angle 3.51325 ( 27) link_NAG-ASN : bond 0.00105 ( 33) link_NAG-ASN : angle 2.03813 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9107 (mtpp) REVERT: A 279 ASP cc_start: 0.8083 (t70) cc_final: 0.7864 (t70) REVERT: A 479 TRP cc_start: 0.7819 (m100) cc_final: 0.7064 (m100) REVERT: A 482 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6581 (mm-30) REVERT: C 63 ASP cc_start: 0.8785 (t0) cc_final: 0.8375 (p0) REVERT: C 92 GLU cc_start: 0.7917 (mp0) cc_final: 0.7651 (pm20) REVERT: D 69 TRP cc_start: 0.7660 (t60) cc_final: 0.7213 (t60) REVERT: D 217 TYR cc_start: 0.5693 (m-80) cc_final: 0.5407 (m-80) REVERT: D 231 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9083 (mmmm) REVERT: D 373 THR cc_start: 0.7569 (t) cc_final: 0.7182 (t) REVERT: D 482 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6687 (tp30) REVERT: E 530 MET cc_start: 0.7568 (mtm) cc_final: 0.7243 (mtm) REVERT: F 63 ASP cc_start: 0.8985 (t0) cc_final: 0.8511 (p0) REVERT: G 279 ASP cc_start: 0.8170 (t70) cc_final: 0.7930 (t70) REVERT: G 373 THR cc_start: 0.7580 (t) cc_final: 0.7254 (t) REVERT: G 479 TRP cc_start: 0.7400 (m100) cc_final: 0.7150 (m100) REVERT: G 482 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6743 (mm-30) REVERT: H 530 MET cc_start: 0.7677 (mtm) cc_final: 0.6520 (mtm) REVERT: H 647 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8518 (tm-30) REVERT: I 51 LEU cc_start: 0.7998 (mm) cc_final: 0.7340 (mp) REVERT: I 54 ARG cc_start: 0.6845 (mpp80) cc_final: 0.6644 (mpp80) REVERT: I 73 ASN cc_start: 0.9137 (t0) cc_final: 0.8935 (t0) outliers start: 56 outliers final: 27 residues processed: 238 average time/residue: 0.1215 time to fit residues: 42.1116 Evaluate side-chains 193 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN H 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.119301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.102273 restraints weight = 44074.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.105755 restraints weight = 22952.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.108129 restraints weight = 14368.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.109764 restraints weight = 10062.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.110934 restraints weight = 7629.355| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14580 Z= 0.164 Angle : 0.731 8.151 19851 Z= 0.366 Chirality : 0.045 0.161 2358 Planarity : 0.004 0.047 2427 Dihedral : 7.326 59.995 2805 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.04 % Allowed : 12.54 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1653 helix: 1.56 (0.26), residues: 405 sheet: -0.15 (0.25), residues: 354 loop : -0.46 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 59 TYR 0.015 0.002 TYR D 486 PHE 0.028 0.002 PHE F 26 TRP 0.030 0.002 TRP I 28 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.00366 (14502) covalent geometry : angle 0.70457 (19647) SS BOND : bond 0.00815 ( 30) SS BOND : angle 1.43899 ( 60) hydrogen bonds : bond 0.05001 ( 576) hydrogen bonds : angle 4.97627 ( 1557) link_ALPHA1-2 : bond 0.00218 ( 3) link_ALPHA1-2 : angle 1.71803 ( 9) link_ALPHA1-3 : bond 0.01205 ( 3) link_ALPHA1-3 : angle 1.64605 ( 9) link_BETA1-4 : bond 0.00225 ( 9) link_BETA1-4 : angle 3.29477 ( 27) link_NAG-ASN : bond 0.00219 ( 33) link_NAG-ASN : angle 1.96206 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7163 (OUTLIER) cc_final: 0.6513 (m-10) REVERT: A 231 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8957 (mmtp) REVERT: A 279 ASP cc_start: 0.8233 (t70) cc_final: 0.7925 (t70) REVERT: A 449 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7004 (pt) REVERT: A 479 TRP cc_start: 0.7411 (m100) cc_final: 0.7155 (m100) REVERT: A 482 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6707 (mm-30) REVERT: B 530 MET cc_start: 0.7639 (mtm) cc_final: 0.7348 (mtm) REVERT: C 92 GLU cc_start: 0.8110 (mp0) cc_final: 0.7876 (pm20) REVERT: D 231 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9056 (mmmm) REVERT: D 279 ASP cc_start: 0.8134 (t70) cc_final: 0.7832 (t70) REVERT: D 449 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.6933 (pt) REVERT: D 482 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6835 (tp30) REVERT: E 530 MET cc_start: 0.7555 (mtm) cc_final: 0.6940 (mtm) REVERT: E 647 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 63 ASP cc_start: 0.9038 (t0) cc_final: 0.8571 (p0) REVERT: G 231 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9031 (mtpp) REVERT: G 279 ASP cc_start: 0.8296 (t70) cc_final: 0.7944 (t70) REVERT: G 373 THR cc_start: 0.7721 (t) cc_final: 0.7344 (t) REVERT: G 449 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.6966 (pt) REVERT: G 479 TRP cc_start: 0.7369 (m100) cc_final: 0.7112 (m100) REVERT: G 482 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6763 (mm-30) REVERT: H 530 MET cc_start: 0.7685 (mtm) cc_final: 0.7008 (mtm) REVERT: H 542 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8647 (ttm110) REVERT: H 647 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8504 (tm-30) outliers start: 46 outliers final: 31 residues processed: 219 average time/residue: 0.1208 time to fit residues: 39.4794 Evaluate side-chains 198 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 657 GLU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.119505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.102283 restraints weight = 43959.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.105750 restraints weight = 23112.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.108113 restraints weight = 14568.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.109740 restraints weight = 10294.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.110871 restraints weight = 7872.752| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14580 Z= 0.140 Angle : 0.684 8.068 19851 Z= 0.344 Chirality : 0.044 0.169 2358 Planarity : 0.004 0.043 2427 Dihedral : 6.614 51.083 2805 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.83 % Allowed : 12.08 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1653 helix: 1.62 (0.26), residues: 405 sheet: 0.01 (0.27), residues: 303 loop : -0.53 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 59 TYR 0.013 0.002 TYR D 217 PHE 0.034 0.002 PHE C 26 TRP 0.030 0.002 TRP I 28 HIS 0.004 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00312 (14502) covalent geometry : angle 0.66050 (19647) SS BOND : bond 0.00468 ( 30) SS BOND : angle 1.39297 ( 60) hydrogen bonds : bond 0.04641 ( 576) hydrogen bonds : angle 4.90402 ( 1557) link_ALPHA1-2 : bond 0.00035 ( 3) link_ALPHA1-2 : angle 1.65540 ( 9) link_ALPHA1-3 : bond 0.00981 ( 3) link_ALPHA1-3 : angle 1.06076 ( 9) link_BETA1-4 : bond 0.00274 ( 9) link_BETA1-4 : angle 3.06618 ( 27) link_NAG-ASN : bond 0.00098 ( 33) link_NAG-ASN : angle 1.77279 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: A 217 TYR cc_start: 0.7563 (m-80) cc_final: 0.6697 (m-80) REVERT: A 231 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9005 (mmtp) REVERT: A 279 ASP cc_start: 0.8068 (t70) cc_final: 0.7743 (t70) REVERT: A 449 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6990 (pt) REVERT: A 479 TRP cc_start: 0.7407 (m100) cc_final: 0.7118 (m100) REVERT: A 482 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 530 MET cc_start: 0.7894 (mtm) cc_final: 0.7324 (mtm) REVERT: C 63 ASP cc_start: 0.8933 (t0) cc_final: 0.8455 (p0) REVERT: D 231 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9058 (mmmm) REVERT: D 279 ASP cc_start: 0.8120 (t70) cc_final: 0.7773 (t70) REVERT: D 373 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7189 (t) REVERT: D 449 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6888 (pt) REVERT: D 482 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6819 (tp30) REVERT: E 626 MET cc_start: 0.6392 (mtp) cc_final: 0.5854 (ttm) REVERT: E 647 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8332 (tm-30) REVERT: F 54 ARG cc_start: 0.6650 (mpp80) cc_final: 0.6445 (mpp80) REVERT: F 59 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7312 (mtp-110) REVERT: F 63 ASP cc_start: 0.9075 (t0) cc_final: 0.8499 (p0) REVERT: F 64 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7999 (mm-40) REVERT: G 231 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9049 (mmmm) REVERT: G 279 ASP cc_start: 0.8223 (t70) cc_final: 0.7865 (t70) REVERT: G 373 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7229 (t) REVERT: G 449 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6954 (pt) REVERT: G 475 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5876 (mmm) REVERT: G 479 TRP cc_start: 0.7340 (m100) cc_final: 0.7120 (m100) REVERT: G 482 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6788 (mm-30) REVERT: H 530 MET cc_start: 0.7764 (mtm) cc_final: 0.6999 (mtm) REVERT: H 570 VAL cc_start: 0.7971 (m) cc_final: 0.7728 (p) REVERT: H 626 MET cc_start: 0.6405 (mtp) cc_final: 0.4951 (ttm) REVERT: H 647 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8421 (tm-30) REVERT: H 656 ASN cc_start: 0.9001 (m-40) cc_final: 0.8584 (m-40) outliers start: 58 outliers final: 34 residues processed: 237 average time/residue: 0.1136 time to fit residues: 40.7062 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 90 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 428 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 = 0.4673 r_free = 0.4673 target = 0.120394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.103272 restraints weight = 43692.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.106800 restraints weight = 22905.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.109232 restraints weight = 14353.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.110903 restraints weight = 10039.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.111987 restraints weight = 7606.888| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14580 Z= 0.124 Angle : 0.680 9.213 19851 Z= 0.340 Chirality : 0.043 0.160 2358 Planarity : 0.004 0.039 2427 Dihedral : 6.206 48.414 2805 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.43 % Allowed : 13.73 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1653 helix: 1.58 (0.26), residues: 405 sheet: 0.08 (0.27), residues: 327 loop : -0.50 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 542 TYR 0.013 0.001 TYR A 486 PHE 0.027 0.002 PHE C 26 TRP 0.056 0.002 TRP I 28 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00278 (14502) covalent geometry : angle 0.65928 (19647) SS BOND : bond 0.00410 ( 30) SS BOND : angle 1.12224 ( 60) hydrogen bonds : bond 0.04444 ( 576) hydrogen bonds : angle 4.77505 ( 1557) link_ALPHA1-2 : bond 0.00174 ( 3) link_ALPHA1-2 : angle 1.68477 ( 9) link_ALPHA1-3 : bond 0.01052 ( 3) link_ALPHA1-3 : angle 1.02239 ( 9) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 2.97003 ( 27) link_NAG-ASN : bond 0.00101 ( 33) link_NAG-ASN : angle 1.70527 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.8047 (t70) cc_final: 0.7711 (t70) REVERT: A 446 SER cc_start: 0.8810 (t) cc_final: 0.8578 (p) REVERT: A 449 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7001 (pt) REVERT: A 479 TRP cc_start: 0.7320 (m100) cc_final: 0.7068 (m100) REVERT: A 482 GLU cc_start: 0.7573 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 530 MET cc_start: 0.7860 (mtm) cc_final: 0.7263 (mtm) REVERT: C 63 ASP cc_start: 0.8950 (t0) cc_final: 0.8484 (p0) REVERT: D 104 MET cc_start: 0.8387 (tpt) cc_final: 0.7582 (mmm) REVERT: D 231 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9072 (mmmm) REVERT: D 279 ASP cc_start: 0.8071 (t70) cc_final: 0.7713 (t70) REVERT: D 373 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7026 (t) REVERT: D 449 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6908 (pt) REVERT: D 479 TRP cc_start: 0.7407 (m100) cc_final: 0.7202 (m100) REVERT: D 482 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6817 (tp30) REVERT: E 530 MET cc_start: 0.7708 (mtm) cc_final: 0.7175 (mtm) REVERT: E 626 MET cc_start: 0.6325 (mtp) cc_final: 0.5651 (ttm) REVERT: E 647 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8295 (tm-30) REVERT: F 54 ARG cc_start: 0.6724 (mpp80) cc_final: 0.6383 (mpp80) REVERT: F 63 ASP cc_start: 0.9065 (t0) cc_final: 0.8525 (p0) REVERT: F 64 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8058 (mm-40) REVERT: G 231 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9096 (mmmm) REVERT: G 279 ASP cc_start: 0.8165 (t70) cc_final: 0.7799 (t70) REVERT: G 373 THR cc_start: 0.7542 (t) cc_final: 0.7144 (t) REVERT: G 426 MET cc_start: 0.7538 (mtm) cc_final: 0.7312 (mtp) REVERT: G 449 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6882 (pt) REVERT: G 475 MET cc_start: 0.6156 (mmp) cc_final: 0.5803 (mmp) REVERT: G 479 TRP cc_start: 0.7323 (m100) cc_final: 0.7112 (m100) REVERT: G 482 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6705 (mm-30) REVERT: H 530 MET cc_start: 0.7654 (mtm) cc_final: 0.6902 (mtm) REVERT: H 570 VAL cc_start: 0.7897 (m) cc_final: 0.7656 (p) REVERT: H 647 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 52 outliers final: 32 residues processed: 233 average time/residue: 0.1063 time to fit residues: 37.6216 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 231 LYS Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 93 optimal weight: 0.0070 chunk 147 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 428 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 = 0.4596 r_free = 0.4596 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.099153 restraints weight = 44813.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.102476 restraints weight = 23498.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.104781 restraints weight = 14898.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.106369 restraints weight = 10590.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.107492 restraints weight = 8129.196| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14580 Z= 0.192 Angle : 0.735 10.490 19851 Z= 0.369 Chirality : 0.045 0.201 2358 Planarity : 0.004 0.041 2427 Dihedral : 6.373 43.119 2805 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.09 % Allowed : 13.47 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1653 helix: 1.31 (0.26), residues: 408 sheet: -0.05 (0.28), residues: 303 loop : -0.70 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 542 TYR 0.012 0.002 TYR G 40 PHE 0.022 0.003 PHE C 26 TRP 0.042 0.002 TRP F 28 HIS 0.007 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00437 (14502) covalent geometry : angle 0.71329 (19647) SS BOND : bond 0.00600 ( 30) SS BOND : angle 1.25511 ( 60) hydrogen bonds : bond 0.04860 ( 576) hydrogen bonds : angle 5.05301 ( 1557) link_ALPHA1-2 : bond 0.00216 ( 3) link_ALPHA1-2 : angle 1.63414 ( 9) link_ALPHA1-3 : bond 0.00810 ( 3) link_ALPHA1-3 : angle 1.15690 ( 9) link_BETA1-4 : bond 0.00238 ( 9) link_BETA1-4 : angle 2.95084 ( 27) link_NAG-ASN : bond 0.00298 ( 33) link_NAG-ASN : angle 1.90333 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7210 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: A 217 TYR cc_start: 0.7587 (m-80) cc_final: 0.7254 (m-80) REVERT: A 279 ASP cc_start: 0.8176 (t70) cc_final: 0.7793 (t0) REVERT: A 446 SER cc_start: 0.8875 (t) cc_final: 0.8644 (p) REVERT: A 449 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7083 (pt) REVERT: A 479 TRP cc_start: 0.7385 (m100) cc_final: 0.7098 (m100) REVERT: A 482 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6982 (mm-30) REVERT: B 530 MET cc_start: 0.7993 (mtm) cc_final: 0.7320 (mtm) REVERT: B 570 VAL cc_start: 0.8111 (m) cc_final: 0.7897 (p) REVERT: C 92 GLU cc_start: 0.8097 (mp0) cc_final: 0.7888 (pm20) REVERT: D 104 MET cc_start: 0.8547 (tpt) cc_final: 0.7946 (tpt) REVERT: D 231 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9044 (mmmm) REVERT: D 279 ASP cc_start: 0.8136 (t70) cc_final: 0.7762 (t70) REVERT: D 373 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7382 (t) REVERT: D 449 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6914 (pt) REVERT: D 482 GLU cc_start: 0.7692 (mm-30) cc_final: 0.6934 (mm-30) REVERT: E 530 MET cc_start: 0.7966 (mtm) cc_final: 0.7467 (mtm) REVERT: E 626 MET cc_start: 0.6633 (mtp) cc_final: 0.5917 (ttm) REVERT: E 647 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 63 ASP cc_start: 0.9111 (t0) cc_final: 0.8602 (p0) REVERT: G 45 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6062 (m-10) REVERT: G 279 ASP cc_start: 0.8278 (t70) cc_final: 0.7871 (t0) REVERT: G 426 MET cc_start: 0.7649 (mtm) cc_final: 0.7413 (mtp) REVERT: G 446 SER cc_start: 0.8856 (t) cc_final: 0.8591 (p) REVERT: G 475 MET cc_start: 0.6456 (mmp) cc_final: 0.6069 (mmp) REVERT: G 479 TRP cc_start: 0.7462 (m100) cc_final: 0.7199 (m100) REVERT: G 482 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6870 (mm-30) REVERT: H 530 MET cc_start: 0.7851 (mtm) cc_final: 0.7056 (mtm) REVERT: H 570 VAL cc_start: 0.8071 (m) cc_final: 0.7868 (p) REVERT: H 626 MET cc_start: 0.6481 (mtp) cc_final: 0.5220 (ttm) REVERT: H 647 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8474 (tm-30) outliers start: 62 outliers final: 44 residues processed: 226 average time/residue: 0.1100 time to fit residues: 37.5839 Evaluate side-chains 212 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 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 = 0.4578 r_free = 0.4578 target = 0.115164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.098142 restraints weight = 44710.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.101419 restraints weight = 23692.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.103686 restraints weight = 15107.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.105263 restraints weight = 10788.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.106330 restraints weight = 8315.843| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14580 Z= 0.199 Angle : 0.752 9.703 19851 Z= 0.378 Chirality : 0.046 0.216 2358 Planarity : 0.004 0.043 2427 Dihedral : 6.426 40.608 2805 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.83 % Allowed : 14.39 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.20), residues: 1653 helix: 1.18 (0.25), residues: 408 sheet: -0.35 (0.28), residues: 339 loop : -0.73 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 59 TYR 0.011 0.002 TYR G 39 PHE 0.023 0.003 PHE C 26 TRP 0.041 0.003 TRP F 28 HIS 0.007 0.001 HIS I 27 Details of bonding type rmsd covalent geometry : bond 0.00454 (14502) covalent geometry : angle 0.73111 (19647) SS BOND : bond 0.00632 ( 30) SS BOND : angle 1.31543 ( 60) hydrogen bonds : bond 0.04930 ( 576) hydrogen bonds : angle 5.17072 ( 1557) link_ALPHA1-2 : bond 0.00090 ( 3) link_ALPHA1-2 : angle 1.68595 ( 9) link_ALPHA1-3 : bond 0.00768 ( 3) link_ALPHA1-3 : angle 1.15114 ( 9) link_BETA1-4 : bond 0.00301 ( 9) link_BETA1-4 : angle 2.91839 ( 27) link_NAG-ASN : bond 0.00280 ( 33) link_NAG-ASN : angle 1.92685 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: A 217 TYR cc_start: 0.7593 (m-80) cc_final: 0.7315 (m-80) REVERT: A 279 ASP cc_start: 0.8193 (t70) cc_final: 0.7801 (t0) REVERT: A 446 SER cc_start: 0.8886 (t) cc_final: 0.8679 (p) REVERT: A 479 TRP cc_start: 0.7399 (m100) cc_final: 0.7137 (m100) REVERT: A 482 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7010 (mm-30) REVERT: B 530 MET cc_start: 0.7957 (mtm) cc_final: 0.7605 (mtm) REVERT: B 570 VAL cc_start: 0.8126 (m) cc_final: 0.7920 (p) REVERT: C 54 ARG cc_start: 0.7178 (mpp80) cc_final: 0.6888 (mpp80) REVERT: D 231 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9005 (mmmm) REVERT: D 279 ASP cc_start: 0.8156 (t70) cc_final: 0.7772 (t70) REVERT: D 373 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 426 MET cc_start: 0.8171 (mtm) cc_final: 0.7898 (pmm) REVERT: D 482 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7000 (mm-30) REVERT: E 530 MET cc_start: 0.7947 (mtm) cc_final: 0.7410 (mtm) REVERT: E 626 MET cc_start: 0.6697 (mtp) cc_final: 0.6107 (ttm) REVERT: E 647 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8483 (tm-30) REVERT: F 63 ASP cc_start: 0.9148 (t0) cc_final: 0.8592 (p0) REVERT: G 45 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6017 (m-10) REVERT: G 279 ASP cc_start: 0.8307 (t70) cc_final: 0.7889 (t0) REVERT: G 426 MET cc_start: 0.7440 (mtm) cc_final: 0.6822 (mtp) REVERT: G 446 SER cc_start: 0.8883 (t) cc_final: 0.8631 (p) REVERT: G 475 MET cc_start: 0.6469 (mmp) cc_final: 0.6086 (mmp) REVERT: G 479 TRP cc_start: 0.7474 (m100) cc_final: 0.7222 (m100) REVERT: G 482 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6903 (mm-30) REVERT: H 530 MET cc_start: 0.7925 (mtm) cc_final: 0.7078 (mtm) REVERT: H 626 MET cc_start: 0.6572 (mtp) cc_final: 0.5327 (ttm) REVERT: H 647 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 58 outliers final: 50 residues processed: 210 average time/residue: 0.1060 time to fit residues: 34.6000 Evaluate side-chains 213 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 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 = 0.4563 r_free = 0.4563 target = 0.114388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.097527 restraints weight = 45151.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.100750 restraints weight = 23793.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.103006 restraints weight = 15137.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.104550 restraints weight = 10797.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.105653 restraints weight = 8328.037| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14580 Z= 0.199 Angle : 0.747 8.956 19851 Z= 0.378 Chirality : 0.046 0.209 2358 Planarity : 0.004 0.043 2427 Dihedral : 6.490 38.694 2805 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.89 % Allowed : 14.26 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1653 helix: 1.04 (0.25), residues: 408 sheet: -0.30 (0.29), residues: 324 loop : -0.98 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 59 TYR 0.012 0.002 TYR D 384 PHE 0.022 0.003 PHE C 26 TRP 0.047 0.003 TRP A 338 HIS 0.007 0.001 HIS I 27 Details of bonding type rmsd covalent geometry : bond 0.00455 (14502) covalent geometry : angle 0.72473 (19647) SS BOND : bond 0.00588 ( 30) SS BOND : angle 1.35070 ( 60) hydrogen bonds : bond 0.04985 ( 576) hydrogen bonds : angle 5.21183 ( 1557) link_ALPHA1-2 : bond 0.00038 ( 3) link_ALPHA1-2 : angle 1.71193 ( 9) link_ALPHA1-3 : bond 0.00676 ( 3) link_ALPHA1-3 : angle 1.09193 ( 9) link_BETA1-4 : bond 0.00307 ( 9) link_BETA1-4 : angle 2.87861 ( 27) link_NAG-ASN : bond 0.00289 ( 33) link_NAG-ASN : angle 1.95924 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7152 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: A 107 ASP cc_start: 0.8493 (t70) cc_final: 0.8229 (t70) REVERT: A 217 TYR cc_start: 0.7604 (m-80) cc_final: 0.7342 (m-80) REVERT: A 279 ASP cc_start: 0.8226 (t70) cc_final: 0.7828 (t0) REVERT: A 446 SER cc_start: 0.8897 (t) cc_final: 0.8682 (p) REVERT: A 479 TRP cc_start: 0.7343 (m100) cc_final: 0.7066 (m100) REVERT: A 482 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 530 MET cc_start: 0.8019 (mtm) cc_final: 0.7300 (mtm) REVERT: B 570 VAL cc_start: 0.8056 (m) cc_final: 0.7855 (p) REVERT: C 54 ARG cc_start: 0.7283 (mpp80) cc_final: 0.7001 (mpp80) REVERT: C 63 ASP cc_start: 0.8761 (t0) cc_final: 0.8268 (p0) REVERT: D 231 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9047 (mmmm) REVERT: D 279 ASP cc_start: 0.8197 (t70) cc_final: 0.7808 (t70) REVERT: D 426 MET cc_start: 0.8049 (mtm) cc_final: 0.7668 (pmm) REVERT: D 482 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7014 (mm-30) REVERT: E 530 MET cc_start: 0.7962 (mtm) cc_final: 0.7450 (mtm) REVERT: E 626 MET cc_start: 0.6722 (mtp) cc_final: 0.6177 (ttm) REVERT: E 647 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8490 (tm-30) REVERT: F 54 ARG cc_start: 0.7325 (mpp80) cc_final: 0.7030 (mpp80) REVERT: F 63 ASP cc_start: 0.9160 (t0) cc_final: 0.8623 (p0) REVERT: G 45 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.5973 (m-10) REVERT: G 279 ASP cc_start: 0.8346 (t70) cc_final: 0.7935 (t0) REVERT: G 426 MET cc_start: 0.7582 (mtm) cc_final: 0.6927 (mtp) REVERT: G 446 SER cc_start: 0.8922 (t) cc_final: 0.8671 (p) REVERT: G 482 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6884 (mm-30) REVERT: H 530 MET cc_start: 0.7913 (mtm) cc_final: 0.7049 (mtm) REVERT: H 626 MET cc_start: 0.6682 (mtp) cc_final: 0.5495 (ttm) REVERT: H 647 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8569 (tm-30) outliers start: 59 outliers final: 51 residues processed: 212 average time/residue: 0.1100 time to fit residues: 36.0121 Evaluate side-chains 212 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 587 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.099048 restraints weight = 44778.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.102361 restraints weight = 23441.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.104675 restraints weight = 14879.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.106275 restraints weight = 10553.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.107405 restraints weight = 8081.791| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14580 Z= 0.152 Angle : 0.726 10.032 19851 Z= 0.363 Chirality : 0.045 0.256 2358 Planarity : 0.004 0.040 2427 Dihedral : 6.207 36.087 2805 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.56 % Allowed : 14.92 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1653 helix: 1.27 (0.25), residues: 405 sheet: -0.11 (0.29), residues: 309 loop : -0.94 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 59 TYR 0.012 0.002 TYR A 486 PHE 0.023 0.002 PHE C 26 TRP 0.039 0.002 TRP F 28 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00348 (14502) covalent geometry : angle 0.70672 (19647) SS BOND : bond 0.00551 ( 30) SS BOND : angle 1.24316 ( 60) hydrogen bonds : bond 0.04651 ( 576) hydrogen bonds : angle 5.07038 ( 1557) link_ALPHA1-2 : bond 0.00010 ( 3) link_ALPHA1-2 : angle 1.68651 ( 9) link_ALPHA1-3 : bond 0.00718 ( 3) link_ALPHA1-3 : angle 1.03874 ( 9) link_BETA1-4 : bond 0.00290 ( 9) link_BETA1-4 : angle 2.75505 ( 27) link_NAG-ASN : bond 0.00139 ( 33) link_NAG-ASN : angle 1.79468 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.7607 (m-80) cc_final: 0.7336 (m-80) REVERT: A 279 ASP cc_start: 0.8174 (t70) cc_final: 0.7790 (t0) REVERT: A 446 SER cc_start: 0.8838 (t) cc_final: 0.8632 (p) REVERT: A 479 TRP cc_start: 0.7232 (m100) cc_final: 0.7011 (m100) REVERT: A 482 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 530 MET cc_start: 0.7996 (mtm) cc_final: 0.7519 (mtm) REVERT: B 570 VAL cc_start: 0.7992 (m) cc_final: 0.7784 (p) REVERT: B 584 GLU cc_start: 0.8257 (pm20) cc_final: 0.8000 (pm20) REVERT: B 626 MET cc_start: 0.6889 (mtt) cc_final: 0.6533 (ttm) REVERT: C 54 ARG cc_start: 0.7210 (mpp80) cc_final: 0.6956 (mpp80) REVERT: C 63 ASP cc_start: 0.8726 (t0) cc_final: 0.8116 (p0) REVERT: D 231 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9113 (mmmm) REVERT: D 279 ASP cc_start: 0.8196 (t70) cc_final: 0.7815 (t70) REVERT: D 373 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7233 (t) REVERT: D 426 MET cc_start: 0.8059 (mtm) cc_final: 0.7781 (pmm) REVERT: D 482 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7046 (mm-30) REVERT: E 530 MET cc_start: 0.7961 (mtm) cc_final: 0.7428 (mtm) REVERT: E 647 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8453 (tm-30) REVERT: F 54 ARG cc_start: 0.7340 (mpp80) cc_final: 0.7052 (mpp80) REVERT: F 63 ASP cc_start: 0.9166 (t0) cc_final: 0.8649 (p0) REVERT: G 45 TRP cc_start: 0.6965 (OUTLIER) cc_final: 0.6029 (m-10) REVERT: G 279 ASP cc_start: 0.8272 (t70) cc_final: 0.7875 (t0) REVERT: G 373 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7368 (t) REVERT: G 426 MET cc_start: 0.7516 (mtm) cc_final: 0.6829 (mtp) REVERT: G 446 SER cc_start: 0.8890 (t) cc_final: 0.8642 (p) REVERT: G 482 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6889 (mm-30) REVERT: H 530 MET cc_start: 0.7821 (mtm) cc_final: 0.7067 (mtm) REVERT: H 626 MET cc_start: 0.6515 (mtp) cc_final: 0.5651 (ttm) REVERT: H 647 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8506 (tm-30) outliers start: 54 outliers final: 48 residues processed: 213 average time/residue: 0.1084 time to fit residues: 35.7197 Evaluate side-chains 213 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 96 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 209 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 457 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 587 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 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 = 0.4643 r_free = 0.4643 target = 0.118778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.101734 restraints weight = 44173.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.105197 restraints weight = 22724.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.107476 restraints weight = 14196.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.109140 restraints weight = 10067.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.110204 restraints weight = 7692.361| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14580 Z= 0.125 Angle : 0.695 9.071 19851 Z= 0.349 Chirality : 0.044 0.270 2358 Planarity : 0.004 0.040 2427 Dihedral : 5.891 33.928 2805 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.17 % Allowed : 14.98 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1653 helix: 1.28 (0.26), residues: 411 sheet: 0.10 (0.30), residues: 309 loop : -0.84 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 59 TYR 0.013 0.001 TYR A 486 PHE 0.024 0.002 PHE C 26 TRP 0.055 0.002 TRP I 28 HIS 0.003 0.001 HIS G 216 Details of bonding type rmsd covalent geometry : bond 0.00279 (14502) covalent geometry : angle 0.67714 (19647) SS BOND : bond 0.00458 ( 30) SS BOND : angle 1.15024 ( 60) hydrogen bonds : bond 0.04296 ( 576) hydrogen bonds : angle 4.92183 ( 1557) link_ALPHA1-2 : bond 0.00037 ( 3) link_ALPHA1-2 : angle 1.67871 ( 9) link_ALPHA1-3 : bond 0.00735 ( 3) link_ALPHA1-3 : angle 1.03424 ( 9) link_BETA1-4 : bond 0.00332 ( 9) link_BETA1-4 : angle 2.63145 ( 27) link_NAG-ASN : bond 0.00094 ( 33) link_NAG-ASN : angle 1.67643 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.78 seconds wall clock time: 43 minutes 35.48 seconds (2615.48 seconds total)