Starting phenix.real_space_refine on Sat Sep 12 07:22:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6opn_20150/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.cif" model { file = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6opn_20150/09_2026/6opn_20150.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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: 2.90, 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: 0.89 Conformation dependent library (CDL) restraints added in 424.6 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: 0.47 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: 2.13 Time building geometry restraints manager: 1.17 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 - 17.18: 8013 17.18 - 34.35: 264 34.35 - 51.52: 63 51.52 - 68.70: 27 68.70 - 85.87: 15 Dihedral angle restraints: 8382 sinusoidal: 3462 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 8379 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: 0.04 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: 1.700 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 10.465 85.020 5088 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/Z covalent geometry : bond 0.02168 / 1.16 (14502) covalent geometry : angle 1.78131 / 1.15 (19647) SS BOND : bond 0.05837 / 4.29 ( 30) SS BOND : angle 2.72245 / 2.05 ( 60) hydrogen bonds : bond 0.19013 / 12.68 ( 576) hydrogen bonds : angle 7.34093 / 5.22 ( 1557) link_ALPHA1-2 : bond 0.04481 / 1.99 ( 3) link_ALPHA1-2 : angle 3.35222 / 2.19 ( 9) link_ALPHA1-3 : bond 0.03369 / 1.51 ( 3) link_ALPHA1-3 : angle 2.19136 / 1.43 ( 9) link_BETA1-4 : bond 0.03345 / 2.16 ( 9) link_BETA1-4 : angle 4.90453 / 3.00 ( 27) link_NAG-ASN : bond 0.03369 / 2.03 ( 33) link_NAG-ASN : angle 3.43507 / 2.42 ( 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 : 0.572 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: 0.1248 time to fit residues: 73.2230 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 : 0.618 ------------------------------------------------------------------------------- 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... 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 = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.103517 restraints weight = 42297.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.107069 restraints weight = 21644.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.109550 restraints weight = 13266.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.111246 restraints weight = 9099.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.112312 restraints weight = 6755.614| |-----------------------------------------------------------------------------| r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14580 Z= 0.218 Angle : 0.886 9.249 19851 Z= 0.453 Chirality : 0.050 0.189 2358 Planarity : 0.005 0.058 2427 Dihedral : 5.957 51.873 1803 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.63 % Allowed : 9.37 % Favored : 87.00 % 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: 0.29 (0.19), residues: 1653 helix: 1.32 (0.26), residues: 405 sheet: 0.09 (0.24), residues: 348 loop : -0.22 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 252 TYR 0.017 0.003 TYR D 486 PHE 0.020 0.003 PHE G 383 TRP 0.024 0.002 TRP G 96 HIS 0.008 0.002 HIS E 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (14502) covalent geometry : angle 0.85393 / 0.45 (19647) SS BOND : bond 0.01274 / 0.64 ( 30) SS BOND : angle 1.65370 / 1.19 ( 60) hydrogen bonds : bond 0.06805 / 4.54 ( 576) hydrogen bonds : angle 5.65530 / 4.09 ( 1557) link_ALPHA1-2 : bond 0.00318 / 0.14 ( 3) link_ALPHA1-2 : angle 1.66391 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00147 / 0.07 ( 3) link_ALPHA1-3 : angle 1.64976 / 1.04 ( 9) link_BETA1-4 : bond 0.00216 / 0.14 ( 9) link_BETA1-4 : angle 3.84382 / 2.41 ( 27) link_NAG-ASN : bond 0.00263 / 0.16 ( 33) link_NAG-ASN : angle 2.57970 / 1.81 ( 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: 55 poor density : 231 time to evaluate : 0.517 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 482 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6623 (mm-30) REVERT: C 1 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7066 (pptt) REVERT: C 51 LEU cc_start: 0.8111 (mm) cc_final: 0.7818 (mp) REVERT: C 73 ASN cc_start: 0.9212 (t0) cc_final: 0.8970 (t0) REVERT: D 69 TRP cc_start: 0.8008 (t60) cc_final: 0.7433 (t-100) REVERT: D 373 THR cc_start: 0.7814 (t) cc_final: 0.7509 (t) REVERT: D 434 MET cc_start: 0.5163 (ttt) cc_final: 0.4959 (ttm) REVERT: D 482 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6840 (tp30) REVERT: E 530 MET cc_start: 0.7613 (mtm) cc_final: 0.7390 (mtp) REVERT: E 592 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6577 (mt) REVERT: G 69 TRP cc_start: 0.8030 (t60) cc_final: 0.7710 (t-100) REVERT: G 217 TYR cc_start: 0.6213 (m-80) cc_final: 0.5814 (m-80) REVERT: G 373 THR cc_start: 0.7864 (t) cc_final: 0.7531 (t) REVERT: G 482 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6688 (mm-30) REVERT: H 530 MET cc_start: 0.7555 (mtm) cc_final: 0.7108 (mtm) REVERT: H 592 LEU cc_start: 0.8259 (mt) cc_final: 0.7346 (mt) REVERT: I 1 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6791 (pptt) REVERT: I 73 ASN cc_start: 0.9204 (t0) cc_final: 0.8970 (t0) REVERT: I 92 GLU cc_start: 0.8256 (pm20) cc_final: 0.8030 (mp0) outliers start: 55 outliers final: 24 residues processed: 272 average time/residue: 0.1208 time to fit residues: 48.2478 Evaluate side-chains 193 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 59 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN A 229 ASN B 652 GLN C 25 GLN D 229 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN G 229 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.118764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.101789 restraints weight = 43217.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.105279 restraints weight = 22165.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.107678 restraints weight = 13715.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.109330 restraints weight = 9508.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.110501 restraints weight = 7154.294| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14580 Z= 0.188 Angle : 0.759 8.081 19851 Z= 0.387 Chirality : 0.046 0.203 2358 Planarity : 0.005 0.050 2427 Dihedral : 5.710 57.681 1803 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.76 % Allowed : 11.16 % Favored : 85.08 % 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: 0.03 (0.19), residues: 1653 helix: 1.40 (0.26), residues: 405 sheet: -0.24 (0.24), residues: 354 loop : -0.47 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.014 0.002 TYR A 484 PHE 0.023 0.003 PHE B 522 TRP 0.040 0.002 TRP F 28 HIS 0.007 0.002 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (14502) covalent geometry : angle 0.73227 / 0.38 (19647) SS BOND : bond 0.00507 / 0.30 ( 30) SS BOND : angle 1.79556 / 1.32 ( 60) hydrogen bonds : bond 0.05657 / 3.77 ( 576) hydrogen bonds : angle 5.25611 / 3.74 ( 1557) link_ALPHA1-2 : bond 0.00176 / 0.08 ( 3) link_ALPHA1-2 : angle 1.56114 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00331 / 0.15 ( 3) link_ALPHA1-3 : angle 1.25302 / 0.74 ( 9) link_BETA1-4 : bond 0.00285 / 0.19 ( 9) link_BETA1-4 : angle 3.13311 / 1.93 ( 27) link_NAG-ASN : bond 0.00216 / 0.12 ( 33) link_NAG-ASN : angle 2.03031 / 1.41 ( 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 244 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.559 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: 0.9480 (OUTLIER) cc_final: 0.9130 (mtpp) REVERT: A 279 ASP cc_start: 0.8223 (t70) cc_final: 0.7997 (t70) REVERT: A 449 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.6955 (pt) REVERT: A 482 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6611 (mm-30) REVERT: C 92 GLU cc_start: 0.7984 (mp0) cc_final: 0.7739 (pm20) REVERT: D 34 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7729 (ptmm) REVERT: D 69 TRP cc_start: 0.7730 (t60) cc_final: 0.7284 (t60) REVERT: D 217 TYR cc_start: 0.5778 (m-80) cc_final: 0.5406 (m-80) REVERT: D 231 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8884 (mmmm) REVERT: D 373 THR cc_start: 0.7771 (t) cc_final: 0.7388 (t) REVERT: D 449 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6873 (pt) REVERT: D 482 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6799 (tp30) REVERT: E 530 MET cc_start: 0.7779 (mtm) cc_final: 0.7473 (mtm) REVERT: F 58 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8325 (mtp85) REVERT: F 63 ASP cc_start: 0.9006 (t0) cc_final: 0.8510 (p0) REVERT: F 92 GLU cc_start: 0.8193 (mp0) cc_final: 0.7956 (pm20) REVERT: G 279 ASP cc_start: 0.8259 (t70) cc_final: 0.8008 (t70) REVERT: G 373 THR cc_start: 0.7789 (t) cc_final: 0.7387 (t) REVERT: G 440 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6620 (tpt170) REVERT: G 449 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6922 (pt) REVERT: G 482 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6787 (mm-30) REVERT: H 530 MET cc_start: 0.7818 (mtm) cc_final: 0.6645 (mtm) REVERT: H 626 MET cc_start: 0.6419 (mtp) cc_final: 0.5670 (mtp) REVERT: H 647 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8638 (tm-30) outliers start: 57 outliers final: 28 residues processed: 230 average time/residue: 0.1215 time to fit residues: 41.1675 Evaluate side-chains 188 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 A residue 457 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 53 ASP 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 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 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 201 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 440 ARG 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 15 THR 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: 6.9990 chunk 94 optimal weight: 4.9990 chunk 42 optimal weight: 0.0040 chunk 165 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 GLN I 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.125282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.106761 restraints weight = 45163.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.110213 restraints weight = 23328.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.112600 restraints weight = 14666.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.114228 restraints weight = 10359.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.115395 restraints weight = 7973.004| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14580 Z= 0.161 Angle : 0.715 8.241 19851 Z= 0.360 Chirality : 0.044 0.163 2358 Planarity : 0.004 0.050 2427 Dihedral : 5.412 52.931 1803 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.37 % Allowed : 12.81 % Favored : 83.83 % 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: -0.02 (0.19), residues: 1653 helix: 1.49 (0.26), residues: 405 sheet: -0.16 (0.26), residues: 327 loop : -0.61 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 59 TYR 0.013 0.002 TYR A 484 PHE 0.030 0.002 PHE F 26 TRP 0.032 0.002 TRP F 28 HIS 0.004 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14502) covalent geometry : angle 0.69193 / 0.36 (19647) SS BOND : bond 0.00602 / 0.40 ( 30) SS BOND : angle 1.65808 / 1.11 ( 60) hydrogen bonds : bond 0.05049 / 3.36 ( 576) hydrogen bonds : angle 5.05019 / 3.61 ( 1557) link_ALPHA1-2 : bond 0.00099 / 0.04 ( 3) link_ALPHA1-2 : angle 1.55476 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00205 / 0.09 ( 3) link_ALPHA1-3 : angle 1.28288 / 0.75 ( 9) link_BETA1-4 : bond 0.00268 / 0.17 ( 9) link_BETA1-4 : angle 2.68552 / 1.66 ( 27) link_NAG-ASN : bond 0.00152 / 0.08 ( 33) link_NAG-ASN : angle 1.83244 / 1.27 ( 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 239 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.384 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 45 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.6732 (m-90) REVERT: A 231 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8915 (mmtp) REVERT: A 279 ASP cc_start: 0.8233 (t70) cc_final: 0.7920 (t70) REVERT: A 449 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6982 (pt) REVERT: A 479 TRP cc_start: 0.7463 (m100) cc_final: 0.7239 (m100) REVERT: A 482 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6763 (mm-30) REVERT: B 530 MET cc_start: 0.7753 (mtm) cc_final: 0.7507 (mtm) REVERT: C 69 LEU cc_start: 0.6566 (mp) cc_final: 0.5759 (tt) REVERT: C 92 GLU cc_start: 0.8155 (mp0) cc_final: 0.7947 (mp0) REVERT: D 231 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8892 (mmmm) REVERT: D 279 ASP cc_start: 0.8147 (t70) cc_final: 0.7818 (t70) REVERT: D 373 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7349 (t) REVERT: D 449 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6894 (pt) REVERT: D 482 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6835 (tp30) REVERT: E 530 MET cc_start: 0.7610 (mtm) cc_final: 0.7018 (mtm) REVERT: E 595 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8229 (pt) REVERT: E 626 MET cc_start: 0.6229 (mtp) cc_final: 0.5407 (ttm) REVERT: F 63 ASP cc_start: 0.9069 (t0) cc_final: 0.8566 (p0) REVERT: F 69 LEU cc_start: 0.7158 (mp) cc_final: 0.6092 (tp) REVERT: G 231 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9087 (mmtp) REVERT: G 279 ASP cc_start: 0.8303 (t70) cc_final: 0.7946 (t70) REVERT: G 373 THR cc_start: 0.7738 (t) cc_final: 0.7310 (t) REVERT: G 426 MET cc_start: 0.7510 (mtm) cc_final: 0.6622 (mtp) REVERT: G 449 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.6905 (pt) REVERT: G 482 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6812 (mm-30) REVERT: H 530 MET cc_start: 0.7754 (mtm) cc_final: 0.6992 (mtm) REVERT: H 647 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8569 (tm-30) outliers start: 51 outliers final: 32 residues processed: 226 average time/residue: 0.1095 time to fit residues: 37.5174 Evaluate side-chains 209 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 B residue 544 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 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 E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 618 THR 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 371 ILE Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 15 THR 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: 5.9990 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.0030 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 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 = 0.4609 r_free = 0.4609 target = 0.116905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.099867 restraints weight = 43389.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.103257 restraints weight = 22545.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.105598 restraints weight = 14126.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.107227 restraints weight = 9914.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.108335 restraints weight = 7534.685| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14580 Z= 0.166 Angle : 0.709 8.318 19851 Z= 0.357 Chirality : 0.044 0.171 2358 Planarity : 0.004 0.045 2427 Dihedral : 5.254 47.983 1803 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.22 % Allowed : 12.74 % Favored : 83.04 % 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: -0.08 (0.19), residues: 1653 helix: 1.45 (0.26), residues: 408 sheet: -0.07 (0.27), residues: 303 loop : -0.71 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 542 TYR 0.012 0.002 TYR A 39 PHE 0.020 0.002 PHE F 26 TRP 0.035 0.002 TRP I 28 HIS 0.006 0.001 HIS F 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (14502) covalent geometry : angle 0.68824 / 0.35 (19647) SS BOND : bond 0.00457 / 0.27 ( 30) SS BOND : angle 1.62927 / 1.09 ( 60) hydrogen bonds : bond 0.04819 / 3.21 ( 576) hydrogen bonds : angle 4.99097 / 3.55 ( 1557) link_ALPHA1-2 : bond 0.00121 / 0.05 ( 3) link_ALPHA1-2 : angle 1.52631 / 0.86 ( 9) link_ALPHA1-3 : bond 0.00207 / 0.10 ( 3) link_ALPHA1-3 : angle 1.29882 / 0.76 ( 9) link_BETA1-4 : bond 0.00290 / 0.18 ( 9) link_BETA1-4 : angle 2.47377 / 1.53 ( 27) link_NAG-ASN : bond 0.00199 / 0.10 ( 33) link_NAG-ASN : angle 1.80506 / 1.24 ( 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 248 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7167 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: A 231 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8971 (mmtp) REVERT: A 279 ASP cc_start: 0.8187 (t70) cc_final: 0.7851 (t70) REVERT: A 446 SER cc_start: 0.8800 (t) cc_final: 0.8596 (p) REVERT: A 449 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7025 (pt) REVERT: A 479 TRP cc_start: 0.7407 (m100) cc_final: 0.7148 (m100) REVERT: A 482 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 530 MET cc_start: 0.7944 (mtm) cc_final: 0.7410 (mtm) REVERT: C 69 LEU cc_start: 0.6226 (mp) cc_final: 0.5868 (tt) REVERT: C 92 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: D 231 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8915 (mmmm) REVERT: D 279 ASP cc_start: 0.8185 (t70) cc_final: 0.7824 (t70) REVERT: D 449 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6935 (pt) REVERT: D 482 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6822 (tp30) REVERT: E 626 MET cc_start: 0.6465 (mtp) cc_final: 0.5856 (ttm) REVERT: F 54 ARG cc_start: 0.6746 (mpp80) cc_final: 0.6464 (mpp80) REVERT: F 63 ASP cc_start: 0.9081 (t0) cc_final: 0.8583 (p0) REVERT: G 279 ASP cc_start: 0.8294 (t70) cc_final: 0.7926 (t70) REVERT: G 373 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7225 (t) REVERT: G 426 MET cc_start: 0.7725 (mtm) cc_final: 0.7052 (mtp) REVERT: G 449 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.6916 (pt) REVERT: G 482 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6854 (mm-30) REVERT: H 530 MET cc_start: 0.7875 (mtm) cc_final: 0.7097 (mtm) REVERT: H 542 ARG cc_start: 0.9058 (mtp-110) cc_final: 0.8690 (ttm110) REVERT: H 626 MET cc_start: 0.6301 (mtp) cc_final: 0.5803 (mtp) REVERT: H 647 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8565 (tm-30) outliers start: 64 outliers final: 43 residues processed: 236 average time/residue: 0.1035 time to fit residues: 37.5257 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 A residue 488 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 615 SER 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 C residue 92 GLU 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 449 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE 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 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 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 15 THR 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: 0.9980 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.118283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.101226 restraints weight = 43917.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.104603 restraints weight = 23017.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.106980 restraints weight = 14532.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.108584 restraints weight = 10196.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.109649 restraints weight = 7791.750| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14580 Z= 0.133 Angle : 0.690 11.421 19851 Z= 0.344 Chirality : 0.044 0.189 2358 Planarity : 0.004 0.048 2427 Dihedral : 5.071 46.173 1803 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.83 % Allowed : 13.73 % 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: 0.00 (0.20), residues: 1653 helix: 1.58 (0.25), residues: 405 sheet: -0.11 (0.28), residues: 303 loop : -0.65 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 542 TYR 0.013 0.001 TYR A 486 PHE 0.018 0.002 PHE F 26 TRP 0.059 0.002 TRP I 28 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14502) covalent geometry : angle 0.67272 / 0.34 (19647) SS BOND : bond 0.00374 / 0.24 ( 30) SS BOND : angle 1.19120 / 0.81 ( 60) hydrogen bonds : bond 0.04535 / 3.00 ( 576) hydrogen bonds : angle 4.92725 / 3.50 ( 1557) link_ALPHA1-2 : bond 0.00088 / 0.04 ( 3) link_ALPHA1-2 : angle 1.49186 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00169 / 0.06 ( 3) link_ALPHA1-3 : angle 1.26773 / 0.72 ( 9) link_BETA1-4 : bond 0.00246 / 0.18 ( 9) link_BETA1-4 : angle 2.36019 / 1.45 ( 27) link_NAG-ASN : bond 0.00094 / 0.04 ( 33) link_NAG-ASN : angle 1.67490 / 1.15 ( 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: 58 poor density : 191 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: A 231 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9023 (mmtp) REVERT: A 279 ASP cc_start: 0.8092 (t70) cc_final: 0.7762 (t70) REVERT: A 449 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7048 (pt) REVERT: A 482 GLU cc_start: 0.7678 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 530 MET cc_start: 0.7894 (mtm) cc_final: 0.7136 (mtm) REVERT: B 570 VAL cc_start: 0.8020 (m) cc_final: 0.7772 (p) REVERT: C 69 LEU cc_start: 0.6312 (mp) cc_final: 0.5840 (tt) REVERT: C 92 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: D 104 MET cc_start: 0.8445 (tpt) cc_final: 0.7881 (tpt) REVERT: D 231 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9014 (mmmm) REVERT: D 279 ASP cc_start: 0.8151 (t70) cc_final: 0.7781 (t70) REVERT: D 373 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7222 (t) REVERT: D 434 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4474 (tmm) REVERT: D 449 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.6915 (pt) REVERT: D 482 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6902 (tp30) REVERT: E 530 MET cc_start: 0.7828 (mtm) cc_final: 0.7213 (mtm) REVERT: E 647 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8369 (tm-30) REVERT: F 54 ARG cc_start: 0.6722 (mpp80) cc_final: 0.6432 (mpp80) REVERT: F 63 ASP cc_start: 0.9081 (t0) cc_final: 0.8601 (p0) REVERT: G 45 TRP cc_start: 0.7025 (OUTLIER) cc_final: 0.6133 (m-10) REVERT: G 279 ASP cc_start: 0.8236 (t70) cc_final: 0.7861 (t70) REVERT: G 373 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7229 (t) REVERT: G 426 MET cc_start: 0.7651 (mtm) cc_final: 0.6968 (mtp) REVERT: G 449 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.6897 (pt) REVERT: G 482 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6804 (mm-30) REVERT: H 530 MET cc_start: 0.7822 (mtm) cc_final: 0.7068 (mtm) REVERT: H 626 MET cc_start: 0.6227 (mtp) cc_final: 0.5532 (mtp) REVERT: H 647 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8473 (tm-30) outliers start: 58 outliers final: 41 residues processed: 233 average time/residue: 0.1008 time to fit residues: 36.4561 Evaluate side-chains 222 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 209 SER 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 A residue 488 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 92 GLU 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 434 MET 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 209 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL 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 645 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 60 SER 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: 2.9990 chunk 159 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 111 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4585 r_free = 0.4585 target = 0.115471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.098478 restraints weight = 44823.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.101776 restraints weight = 23494.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.104076 restraints weight = 14882.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.105618 restraints weight = 10552.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.106748 restraints weight = 8128.395| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14580 Z= 0.184 Angle : 0.720 9.173 19851 Z= 0.362 Chirality : 0.045 0.180 2358 Planarity : 0.004 0.041 2427 Dihedral : 5.094 43.157 1803 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.83 % Allowed : 14.52 % Favored : 81.65 % 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: 1.39 (0.25), residues: 408 sheet: -0.19 (0.28), residues: 333 loop : -0.77 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 542 TYR 0.011 0.002 TYR A 486 PHE 0.018 0.002 PHE B 522 TRP 0.043 0.002 TRP I 28 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14502) covalent geometry : angle 0.70043 / 0.36 (19647) SS BOND : bond 0.00598 / 0.31 ( 30) SS BOND : angle 1.57432 / 1.05 ( 60) hydrogen bonds : bond 0.04856 / 3.23 ( 576) hydrogen bonds : angle 5.09183 / 3.59 ( 1557) link_ALPHA1-2 : bond 0.00073 / 0.03 ( 3) link_ALPHA1-2 : angle 1.52966 / 0.85 ( 9) link_ALPHA1-3 : bond 0.00174 / 0.07 ( 3) link_ALPHA1-3 : angle 1.33122 / 0.80 ( 9) link_BETA1-4 : bond 0.00367 / 0.23 ( 9) link_BETA1-4 : angle 2.27459 / 1.39 ( 27) link_NAG-ASN : bond 0.00260 / 0.13 ( 33) link_NAG-ASN : angle 1.80443 / 1.23 ( 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 229 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.557 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: 0.7116 (OUTLIER) cc_final: 0.6722 (m-10) REVERT: A 231 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9048 (mmtp) REVERT: A 279 ASP cc_start: 0.8151 (t70) cc_final: 0.7776 (t0) REVERT: A 449 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7078 (pt) REVERT: A 482 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 530 MET cc_start: 0.7914 (mtm) cc_final: 0.7220 (mtm) REVERT: B 570 VAL cc_start: 0.8108 (m) cc_final: 0.7883 (p) REVERT: D 104 MET cc_start: 0.8537 (tpt) cc_final: 0.7930 (tpt) REVERT: D 231 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9009 (mmmm) REVERT: D 279 ASP cc_start: 0.8153 (t70) cc_final: 0.7784 (t70) REVERT: D 373 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7430 (t) REVERT: D 449 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.6944 (pt) REVERT: D 482 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6989 (mm-30) REVERT: E 530 MET cc_start: 0.7948 (mtm) cc_final: 0.7438 (mtm) REVERT: E 626 MET cc_start: 0.6868 (mtp) cc_final: 0.6231 (ttm) REVERT: E 647 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 63 ASP cc_start: 0.9113 (t0) cc_final: 0.8599 (p0) REVERT: G 45 TRP cc_start: 0.7123 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: G 279 ASP cc_start: 0.8280 (t70) cc_final: 0.7902 (t70) REVERT: G 373 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7297 (t) REVERT: G 426 MET cc_start: 0.7800 (mtm) cc_final: 0.7171 (mtp) REVERT: G 446 SER cc_start: 0.8912 (t) cc_final: 0.8682 (p) REVERT: G 449 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6993 (pt) REVERT: G 482 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6840 (mm-30) REVERT: H 530 MET cc_start: 0.7826 (mtm) cc_final: 0.7018 (mtm) REVERT: H 626 MET cc_start: 0.6527 (mtp) cc_final: 0.5953 (mtp) REVERT: H 647 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8520 (tm-30) outliers start: 58 outliers final: 44 residues processed: 217 average time/residue: 0.1054 time to fit residues: 35.3233 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 201 ILE Chi-restraints excluded: chain A residue 209 SER 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 A residue 488 VAL 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 595 ILE Chi-restraints excluded: chain E residue 615 SER 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 251 ILE Chi-restraints excluded: chain G residue 254 VAL 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 599 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 60 SER 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: 3.9990 chunk 58 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4646 r_free = 0.4646 target = 0.118889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.101913 restraints weight = 43897.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.105323 restraints weight = 22886.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.107677 restraints weight = 14392.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.109301 restraints weight = 10160.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.110458 restraints weight = 7745.903| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14580 Z= 0.122 Angle : 0.698 10.802 19851 Z= 0.346 Chirality : 0.044 0.256 2358 Planarity : 0.004 0.041 2427 Dihedral : 4.843 41.980 1803 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.43 % Allowed : 15.31 % Favored : 81.25 % 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: 0.05 (0.20), residues: 1653 helix: 1.66 (0.25), residues: 402 sheet: -0.01 (0.28), residues: 336 loop : -0.67 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 273 TYR 0.014 0.001 TYR A 486 PHE 0.017 0.001 PHE F 26 TRP 0.038 0.002 TRP I 28 HIS 0.002 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14502) covalent geometry : angle 0.68347 / 0.34 (19647) SS BOND : bond 0.00544 / 0.27 ( 30) SS BOND : angle 1.21399 / 0.79 ( 60) hydrogen bonds : bond 0.04325 / 2.86 ( 576) hydrogen bonds : angle 4.86246 / 3.41 ( 1557) link_ALPHA1-2 : bond 0.00168 / 0.07 ( 3) link_ALPHA1-2 : angle 1.48964 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00253 / 0.11 ( 3) link_ALPHA1-3 : angle 1.36539 / 0.76 ( 9) link_BETA1-4 : bond 0.00394 / 0.25 ( 9) link_BETA1-4 : angle 2.11398 / 1.32 ( 27) link_NAG-ASN : bond 0.00101 / 0.06 ( 33) link_NAG-ASN : angle 1.58704 / 1.09 ( 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 245 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6525 (m-10) REVERT: A 231 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9066 (mmtp) REVERT: A 279 ASP cc_start: 0.8090 (t70) cc_final: 0.7759 (t70) REVERT: A 449 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6932 (pt) REVERT: A 479 TRP cc_start: 0.7232 (m100) cc_final: 0.6578 (m100) REVERT: A 482 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6945 (mm-30) REVERT: B 530 MET cc_start: 0.7864 (mtm) cc_final: 0.7512 (mtm) REVERT: B 570 VAL cc_start: 0.7903 (m) cc_final: 0.7644 (p) REVERT: D 104 MET cc_start: 0.8397 (tpt) cc_final: 0.7832 (tpt) REVERT: D 231 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9033 (mmmm) REVERT: D 279 ASP cc_start: 0.8071 (t70) cc_final: 0.7714 (t70) REVERT: D 373 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7065 (t) REVERT: D 449 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6864 (pt) REVERT: D 482 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6855 (tp30) REVERT: E 530 MET cc_start: 0.7903 (mtm) cc_final: 0.7309 (mtm) REVERT: E 626 MET cc_start: 0.6806 (mtp) cc_final: 0.6225 (ttm) REVERT: E 647 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8382 (tm-30) REVERT: F 54 ARG cc_start: 0.7080 (mpp80) cc_final: 0.6743 (mpp80) REVERT: F 63 ASP cc_start: 0.9104 (t0) cc_final: 0.8615 (p0) REVERT: G 45 TRP cc_start: 0.6872 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: G 279 ASP cc_start: 0.8155 (t70) cc_final: 0.7787 (t70) REVERT: G 373 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7198 (t) REVERT: G 426 MET cc_start: 0.7611 (mtm) cc_final: 0.6957 (mtp) REVERT: G 446 SER cc_start: 0.8871 (t) cc_final: 0.8655 (p) REVERT: G 449 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6863 (pt) REVERT: G 482 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6810 (mm-30) REVERT: H 530 MET cc_start: 0.7743 (mtm) cc_final: 0.6972 (mtm) REVERT: H 626 MET cc_start: 0.6106 (mtp) cc_final: 0.5531 (mtp) REVERT: H 647 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8410 (tm-30) outliers start: 52 outliers final: 35 residues processed: 227 average time/residue: 0.1063 time to fit residues: 37.3294 Evaluate side-chains 221 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 96 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 A residue 488 VAL 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 96 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 373 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 615 SER 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 45 TRP Chi-restraints excluded: chain G residue 108 ILE 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 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 599 SER Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 15 THR 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: 6.9990 chunk 48 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 152 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN F 39 ASN I 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.112573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.095629 restraints weight = 45168.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.098795 restraints weight = 23682.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.101007 restraints weight = 15087.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.102571 restraints weight = 10775.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.103647 restraints weight = 8321.083| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14580 Z= 0.268 Angle : 0.814 9.377 19851 Z= 0.413 Chirality : 0.047 0.189 2358 Planarity : 0.005 0.077 2427 Dihedral : 5.303 38.889 1803 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.69 % Allowed : 13.86 % Favored : 81.45 % 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: -0.55 (0.19), residues: 1653 helix: 0.99 (0.25), residues: 408 sheet: -0.23 (0.27), residues: 357 loop : -1.07 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 542 TYR 0.018 0.002 TYR D 486 PHE 0.031 0.003 PHE B 522 TRP 0.050 0.003 TRP A 338 HIS 0.008 0.002 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (14502) covalent geometry : angle 0.79303 / 0.41 (19647) SS BOND : bond 0.00648 / 0.35 ( 30) SS BOND : angle 1.78237 / 1.22 ( 60) hydrogen bonds : bond 0.05369 / 3.55 ( 576) hydrogen bonds : angle 5.34580 / 3.78 ( 1557) link_ALPHA1-2 : bond 0.00098 / 0.04 ( 3) link_ALPHA1-2 : angle 1.65743 / 0.91 ( 9) link_ALPHA1-3 : bond 0.00040 / 0.02 ( 3) link_ALPHA1-3 : angle 1.49554 / 0.93 ( 9) link_BETA1-4 : bond 0.00481 / 0.30 ( 9) link_BETA1-4 : angle 2.34711 / 1.41 ( 27) link_NAG-ASN : bond 0.00497 / 0.26 ( 33) link_NAG-ASN : angle 2.06324 / 1.41 ( 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 234 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: A 279 ASP cc_start: 0.8201 (t70) cc_final: 0.7810 (t0) REVERT: A 482 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 530 MET cc_start: 0.8040 (mtm) cc_final: 0.7710 (mtm) REVERT: D 231 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9027 (mmmm) REVERT: D 279 ASP cc_start: 0.8175 (t70) cc_final: 0.7795 (t70) REVERT: D 426 MET cc_start: 0.7741 (pmm) cc_final: 0.7363 (pmm) REVERT: D 482 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7074 (mm-30) REVERT: E 530 MET cc_start: 0.8002 (mtm) cc_final: 0.7491 (mtm) REVERT: E 626 MET cc_start: 0.6893 (mtp) cc_final: 0.6347 (ttm) REVERT: E 647 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8593 (tm-30) REVERT: F 59 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7658 (mtp-110) REVERT: G 45 TRP cc_start: 0.7104 (OUTLIER) cc_final: 0.5982 (m-10) REVERT: G 279 ASP cc_start: 0.8324 (t70) cc_final: 0.7905 (t0) REVERT: G 482 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6876 (mm-30) REVERT: H 647 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8624 (tm-30) REVERT: H 656 ASN cc_start: 0.9098 (m-40) cc_final: 0.8732 (m110) outliers start: 71 outliers final: 59 residues processed: 220 average time/residue: 0.1034 time to fit residues: 34.8084 Evaluate side-chains 217 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 109 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 544 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 37 THR 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 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 599 SER 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 39 ASN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU 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 371 ILE Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 449 ILE 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 H residue 599 SER Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 39 ASN Chi-restraints excluded: chain I residue 60 SER 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: 1.9990 chunk 126 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4577 r_free = 0.4577 target = 0.115024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.098164 restraints weight = 44981.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.101446 restraints weight = 23470.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.103728 restraints weight = 14828.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.105294 restraints weight = 10505.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.106425 restraints weight = 8059.858| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14580 Z= 0.148 Angle : 0.745 10.330 19851 Z= 0.376 Chirality : 0.045 0.187 2358 Planarity : 0.005 0.071 2427 Dihedral : 5.156 39.337 1803 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.97 % Allowed : 15.97 % Favored : 81.06 % 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: -0.46 (0.20), residues: 1653 helix: 1.04 (0.25), residues: 408 sheet: -0.25 (0.29), residues: 330 loop : -0.94 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 542 TYR 0.018 0.002 TYR G 40 PHE 0.017 0.002 PHE B 522 TRP 0.041 0.003 TRP A 338 HIS 0.004 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (14502) covalent geometry : angle 0.72732 / 0.37 (19647) SS BOND : bond 0.00522 / 0.28 ( 30) SS BOND : angle 1.45098 / 0.97 ( 60) hydrogen bonds : bond 0.04989 / 3.31 ( 576) hydrogen bonds : angle 5.16028 / 3.64 ( 1557) link_ALPHA1-2 : bond 0.00152 / 0.07 ( 3) link_ALPHA1-2 : angle 1.56808 / 0.85 ( 9) link_ALPHA1-3 : bond 0.00118 / 0.04 ( 3) link_ALPHA1-3 : angle 1.26778 / 0.73 ( 9) link_BETA1-4 : bond 0.00338 / 0.22 ( 9) link_BETA1-4 : angle 2.17953 / 1.34 ( 27) link_NAG-ASN : bond 0.00172 / 0.08 ( 33) link_NAG-ASN : angle 1.80974 / 1.24 ( 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 208 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.6770 (m-10) REVERT: A 279 ASP cc_start: 0.8153 (t70) cc_final: 0.7769 (t0) REVERT: A 482 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 530 MET cc_start: 0.8014 (mtm) cc_final: 0.7651 (mtm) REVERT: B 656 ASN cc_start: 0.9033 (m-40) cc_final: 0.8735 (m110) REVERT: D 231 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9039 (mmmm) REVERT: D 279 ASP cc_start: 0.8130 (t70) cc_final: 0.7749 (t70) REVERT: D 373 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7415 (t) REVERT: D 426 MET cc_start: 0.7825 (pmm) cc_final: 0.7450 (pmm) REVERT: D 482 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6951 (mm-30) REVERT: E 530 MET cc_start: 0.7965 (mtm) cc_final: 0.7453 (mtm) REVERT: E 626 MET cc_start: 0.6866 (mtp) cc_final: 0.6250 (ttm) REVERT: E 647 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8521 (tm-30) REVERT: F 63 ASP cc_start: 0.8749 (t0) cc_final: 0.8252 (p0) REVERT: G 45 TRP cc_start: 0.6940 (OUTLIER) cc_final: 0.6077 (m-10) REVERT: G 279 ASP cc_start: 0.8255 (t70) cc_final: 0.7836 (t0) REVERT: G 426 MET cc_start: 0.7777 (mtm) cc_final: 0.7117 (mtp) REVERT: G 482 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6779 (mm-30) REVERT: H 530 MET cc_start: 0.8094 (mtm) cc_final: 0.7472 (mtm) REVERT: H 647 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8546 (tm-30) REVERT: H 656 ASN cc_start: 0.9068 (m-40) cc_final: 0.8697 (m110) outliers start: 45 outliers final: 39 residues processed: 203 average time/residue: 0.1092 time to fit residues: 34.0133 Evaluate side-chains 201 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 645 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 74 CYS 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 288 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU 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 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 108 ILE 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 373 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 587 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain H residue 645 LEU Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 60 SER 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: 0.9990 chunk 119 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.116138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.099274 restraints weight = 44446.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.102506 restraints weight = 23242.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.104834 restraints weight = 14764.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.106449 restraints weight = 10458.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.107556 restraints weight = 7995.061| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5644 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= 0.144 Angle : 0.712 9.853 19851 Z= 0.359 Chirality : 0.044 0.183 2358 Planarity : 0.005 0.069 2427 Dihedral : 4.953 37.446 1803 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.23 % Allowed : 15.97 % Favored : 80.79 % 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: 1.35 (0.25), residues: 405 sheet: -0.31 (0.28), residues: 345 loop : -0.84 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 59 TYR 0.014 0.002 TYR D 217 PHE 0.015 0.002 PHE F 26 TRP 0.040 0.003 TRP A 338 HIS 0.005 0.001 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (14502) covalent geometry : angle 0.69691 / 0.36 (19647) SS BOND : bond 0.00498 / 0.27 ( 30) SS BOND : angle 1.29118 / 0.86 ( 60) hydrogen bonds : bond 0.04547 / 3.00 ( 576) hydrogen bonds : angle 4.98599 / 3.51 ( 1557) link_ALPHA1-2 : bond 0.00168 / 0.07 ( 3) link_ALPHA1-2 : angle 1.50024 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00214 / 0.10 ( 3) link_ALPHA1-3 : angle 1.32933 / 0.76 ( 9) link_BETA1-4 : bond 0.00330 / 0.21 ( 9) link_BETA1-4 : angle 2.11280 / 1.31 ( 27) link_NAG-ASN : bond 0.00111 / 0.05 ( 33) link_NAG-ASN : angle 1.67493 / 1.14 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.37 seconds wall clock time: 43 minutes 22.21 seconds (2602.21 seconds total)