Starting phenix.real_space_refine on Wed Mar 4 19:51:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8w_23238/03_2026/7l8w_23238.cif" } resolution = 4.1 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= 0.003 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 105 5.16 5 C 9845 2.51 5 N 2677 2.21 5 O 3176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3485 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1060 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3466 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.64, per 1000 atoms: 0.23 Number of scatterers: 15803 At special positions: 0 Unit cell: (127.72, 136.99, 118.45, 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 105 16.00 O 3176 8.00 N 2677 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.10 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 8 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 9 " " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 160 " " NAG A 613 " - " ASN A 197 " " NAG A 614 " - " ASN A 133 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 137 " " NAG A 617 " - " ASN A 363 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG C 616 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN E 332 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 156 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 654.7 milliseconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 32 sheets defined 31.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.525A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.744A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 661 removed outlier: 3.631A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.504A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.783A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.345A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.084A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.965A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.015A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.762A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.117A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 545 removed outlier: 4.027A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id=AA1, first strand: chain 'A' and resid 495 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 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.687A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.264A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.445A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.334A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.880A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.679A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.753A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.704A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.236A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.698A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.522A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 3.783A pdb=" N ILE E 309 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.778A pdb=" N UNK H 18 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 58 Processing sheet with id=AD3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.561A pdb=" N UNK L 37 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK L 86 " --> pdb=" O UNK L 40 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1797 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: 2.77 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3102 1.32 - 1.46: 5297 1.46 - 1.60: 7510 1.60 - 1.74: 30 1.74 - 1.88: 133 Bond restraints: 16072 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG C 550 " pdb=" CZ ARG C 550 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18523 2.29 - 4.58: 2814 4.58 - 6.87: 469 6.87 - 9.16: 44 9.16 - 11.44: 2 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C PHE C 53 " pdb=" N CYS C 54 " pdb=" CA CYS C 54 " ideal model delta sigma weight residual 122.19 133.63 -11.44 1.41e+00 5.03e-01 6.59e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.01e+00 9.80e-01 6.44e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.05 7.42 9.60e-01 1.09e+00 5.98e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.23 122.33 -9.10 1.24e+00 6.50e-01 5.39e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10478 21.43 - 42.86: 220 42.86 - 64.30: 74 64.30 - 85.73: 33 85.73 - 107.16: 13 Dihedral angle restraints: 10818 sinusoidal: 5229 harmonic: 5589 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.12 -73.12 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 164.19 -71.19 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 10815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2395 0.188 - 0.376: 311 0.376 - 0.565: 64 0.565 - 0.753: 1 0.753 - 0.941: 2 Chirality restraints: 2773 Sorted by residual: chirality pdb=" C1 MAN G 8 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 8 " pdb=" O5 MAN G 8 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.21e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 2770 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 602 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.332 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A 607 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 612 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A 612 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 612 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 612 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG A 612 " 0.060 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5748 2.88 - 3.39: 14373 3.39 - 3.89: 25518 3.89 - 4.40: 29106 4.40 - 4.90: 45961 Nonbonded interactions: 120706 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.378 2.496 nonbonded pdb=" O3 NAG D 703 " pdb=" O7 NAG D 703 " model vdw 2.383 3.040 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.436 3.120 nonbonded pdb=" OD1 ASN E 234 " pdb=" N GLY E 235 " model vdw 2.451 3.120 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.488 3.120 ... (remaining 120701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 64 through 616)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 457 or resid 461 throu \ gh 616)) selection = (chain 'E' and (resid 33 through 57 or resid 64 through 457 or resid 461 through \ 616)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 558 through 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 662 or resid 702 through 703)) } ncs_group { reference = (chain 'H' and resid 8 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'K' 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 0.121 16194 Z= 1.163 Angle : 1.742 11.444 22182 Z= 1.105 Chirality : 0.137 0.941 2773 Planarity : 0.018 0.291 2679 Dihedral : 11.366 107.162 7070 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.14 (0.19), residues: 1678 helix: 0.58 (0.22), residues: 427 sheet: 1.21 (0.23), residues: 465 loop : 0.77 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 542 TYR 0.071 0.008 TYR D 638 PHE 0.039 0.006 PHE A 383 TRP 0.074 0.010 TRP C 35 HIS 0.013 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.02121 (16072) covalent geometry : angle 1.70907 (21852) SS BOND : bond 0.02180 ( 36) SS BOND : angle 3.11253 ( 72) hydrogen bonds : bond 0.17631 ( 650) hydrogen bonds : angle 7.37557 ( 1797) link_ALPHA1-2 : bond 0.05982 ( 2) link_ALPHA1-2 : angle 4.07674 ( 6) link_ALPHA1-3 : bond 0.06061 ( 4) link_ALPHA1-3 : angle 5.03794 ( 12) link_ALPHA1-6 : bond 0.05963 ( 4) link_ALPHA1-6 : angle 3.37177 ( 12) link_BETA1-4 : bond 0.05895 ( 11) link_BETA1-4 : angle 3.99102 ( 33) link_NAG-ASN : bond 0.07109 ( 65) link_NAG-ASN : angle 2.98335 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.664 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: A 199 SER cc_start: 0.9435 (p) cc_final: 0.8935 (t) REVERT: A 257 THR cc_start: 0.8957 (p) cc_final: 0.8658 (m) REVERT: B 591 GLN cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: B 599 SER cc_start: 0.9019 (p) cc_final: 0.8335 (t) REVERT: B 601 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8606 (tptp) REVERT: C 38 VAL cc_start: 0.8541 (t) cc_final: 0.8179 (t) REVERT: C 69 TRP cc_start: 0.8141 (m-10) cc_final: 0.7906 (m-10) REVERT: C 102 GLU cc_start: 0.8251 (tp30) cc_final: 0.7745 (tm-30) REVERT: C 199 SER cc_start: 0.9546 (p) cc_final: 0.9296 (t) REVERT: D 585 ARG cc_start: 0.9197 (mmt180) cc_final: 0.8898 (ttm-80) REVERT: D 586 TYR cc_start: 0.9636 (t80) cc_final: 0.9356 (t80) REVERT: D 623 TRP cc_start: 0.8861 (m100) cc_final: 0.8398 (m-10) REVERT: E 45 TRP cc_start: 0.8802 (p90) cc_final: 0.8589 (p90) REVERT: E 57 ASP cc_start: 0.8224 (t0) cc_final: 0.7884 (p0) REVERT: E 103 GLN cc_start: 0.8566 (tt0) cc_final: 0.8206 (tm-30) REVERT: E 381 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7551 (tt0) REVERT: F 579 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8780 (ttm170) REVERT: F 629 LEU cc_start: 0.9059 (tp) cc_final: 0.8765 (mp) REVERT: F 638 TYR cc_start: 0.8320 (m-80) cc_final: 0.8067 (m-10) REVERT: F 650 GLN cc_start: 0.8917 (tp40) cc_final: 0.7736 (tm-30) REVERT: F 654 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7132 (mt-10) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.1423 time to fit residues: 104.1294 Evaluate side-chains 248 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 302 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 203 GLN E 287 GLN E 300 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093685 restraints weight = 35267.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096448 restraints weight = 20931.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098292 restraints weight = 14621.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099556 restraints weight = 11420.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100423 restraints weight = 9601.840| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16194 Z= 0.190 Angle : 0.861 16.871 22182 Z= 0.412 Chirality : 0.052 0.690 2773 Planarity : 0.004 0.043 2679 Dihedral : 9.716 90.830 3805 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.01 % Favored : 98.93 % Rotamer: Outliers : 0.33 % Allowed : 2.42 % Favored : 97.25 % 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: 1.22 (0.20), residues: 1678 helix: 1.89 (0.25), residues: 426 sheet: 1.08 (0.23), residues: 454 loop : 0.14 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 308 TYR 0.016 0.002 TYR B 643 PHE 0.020 0.002 PHE A 383 TRP 0.026 0.002 TRP A 69 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00406 (16072) covalent geometry : angle 0.78398 (21852) SS BOND : bond 0.00258 ( 36) SS BOND : angle 1.46164 ( 72) hydrogen bonds : bond 0.06354 ( 650) hydrogen bonds : angle 6.10462 ( 1797) link_ALPHA1-2 : bond 0.01034 ( 2) link_ALPHA1-2 : angle 1.90072 ( 6) link_ALPHA1-3 : bond 0.01792 ( 4) link_ALPHA1-3 : angle 2.17235 ( 12) link_ALPHA1-6 : bond 0.01130 ( 4) link_ALPHA1-6 : angle 1.76053 ( 12) link_BETA1-4 : bond 0.01019 ( 11) link_BETA1-4 : angle 2.83632 ( 33) link_NAG-ASN : bond 0.00611 ( 65) link_NAG-ASN : angle 3.55570 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 361 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ILE cc_start: 0.9269 (mm) cc_final: 0.9068 (mm) REVERT: A 209 SER cc_start: 0.8494 (t) cc_final: 0.8015 (p) REVERT: A 475 MET cc_start: 0.8855 (mmm) cc_final: 0.8639 (mmm) REVERT: B 568 LEU cc_start: 0.8430 (mp) cc_final: 0.8171 (mp) REVERT: B 602 LEU cc_start: 0.8730 (mt) cc_final: 0.8383 (pt) REVERT: B 641 ILE cc_start: 0.8020 (mp) cc_final: 0.7299 (tp) REVERT: C 38 VAL cc_start: 0.8463 (t) cc_final: 0.7877 (t) REVERT: C 104 MET cc_start: 0.8618 (ttt) cc_final: 0.8222 (ttt) REVERT: C 114 GLN cc_start: 0.8487 (tp40) cc_final: 0.7570 (tm-30) REVERT: C 199 SER cc_start: 0.9461 (p) cc_final: 0.9166 (t) REVERT: C 286 VAL cc_start: 0.9299 (t) cc_final: 0.9080 (m) REVERT: C 377 ASN cc_start: 0.9153 (t0) cc_final: 0.8852 (t0) REVERT: C 395 TRP cc_start: 0.7675 (m100) cc_final: 0.7444 (m100) REVERT: C 486 TYR cc_start: 0.9050 (m-80) cc_final: 0.8760 (m-80) REVERT: D 565 LEU cc_start: 0.7910 (tp) cc_final: 0.7376 (tp) REVERT: D 577 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 643 TYR cc_start: 0.8942 (m-10) cc_final: 0.8646 (m-80) REVERT: E 51 THR cc_start: 0.9051 (m) cc_final: 0.8649 (p) REVERT: E 103 GLN cc_start: 0.8150 (tt0) cc_final: 0.7693 (tm-30) REVERT: F 543 ASN cc_start: 0.8494 (t0) cc_final: 0.8200 (t0) REVERT: F 590 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8950 (tp40) REVERT: F 629 LEU cc_start: 0.8896 (tp) cc_final: 0.8157 (pp) REVERT: F 634 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8144 (mm-30) REVERT: F 648 GLU cc_start: 0.8329 (tp30) cc_final: 0.8064 (tp30) REVERT: F 650 GLN cc_start: 0.8919 (tp40) cc_final: 0.8372 (tm-30) REVERT: F 652 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8266 (tt0) REVERT: F 653 GLN cc_start: 0.8299 (tt0) cc_final: 0.8070 (tt0) outliers start: 5 outliers final: 2 residues processed: 364 average time/residue: 0.1273 time to fit residues: 68.5290 Evaluate side-chains 245 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 80 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 562 GLN B 658 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 203 GLN F 577 GLN F 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090813 restraints weight = 36114.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093448 restraints weight = 21592.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.095218 restraints weight = 15283.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096307 restraints weight = 12058.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097206 restraints weight = 10322.190| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16194 Z= 0.190 Angle : 0.759 13.584 22182 Z= 0.367 Chirality : 0.049 0.517 2773 Planarity : 0.004 0.042 2679 Dihedral : 8.565 74.967 3805 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % Rotamer: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % 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: 1.03 (0.20), residues: 1678 helix: 1.81 (0.25), residues: 427 sheet: 0.91 (0.24), residues: 431 loop : 0.02 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.021 0.002 TYR B 643 PHE 0.017 0.002 PHE A 383 TRP 0.025 0.002 TRP C 69 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00424 (16072) covalent geometry : angle 0.69760 (21852) SS BOND : bond 0.00552 ( 36) SS BOND : angle 1.53912 ( 72) hydrogen bonds : bond 0.05300 ( 650) hydrogen bonds : angle 5.71675 ( 1797) link_ALPHA1-2 : bond 0.00804 ( 2) link_ALPHA1-2 : angle 2.09029 ( 6) link_ALPHA1-3 : bond 0.01361 ( 4) link_ALPHA1-3 : angle 1.82503 ( 12) link_ALPHA1-6 : bond 0.01201 ( 4) link_ALPHA1-6 : angle 1.45712 ( 12) link_BETA1-4 : bond 0.00678 ( 11) link_BETA1-4 : angle 2.15295 ( 33) link_NAG-ASN : bond 0.00505 ( 65) link_NAG-ASN : angle 2.96977 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8879 (tpp) cc_final: 0.8304 (tpp) REVERT: A 209 SER cc_start: 0.8674 (t) cc_final: 0.8413 (p) REVERT: A 256 SER cc_start: 0.9508 (p) cc_final: 0.9055 (m) REVERT: A 318 TYR cc_start: 0.8765 (m-80) cc_final: 0.8558 (m-80) REVERT: A 475 MET cc_start: 0.8867 (mmm) cc_final: 0.8542 (mmm) REVERT: B 599 SER cc_start: 0.8920 (p) cc_final: 0.8595 (p) REVERT: B 603 ILE cc_start: 0.8288 (mm) cc_final: 0.8073 (tt) REVERT: B 634 GLU cc_start: 0.8028 (pt0) cc_final: 0.7457 (pp20) REVERT: B 641 ILE cc_start: 0.8071 (mp) cc_final: 0.7589 (tp) REVERT: B 643 TYR cc_start: 0.9073 (m-10) cc_final: 0.8778 (m-10) REVERT: C 38 VAL cc_start: 0.8199 (t) cc_final: 0.7756 (t) REVERT: C 199 SER cc_start: 0.9454 (p) cc_final: 0.9160 (t) REVERT: C 286 VAL cc_start: 0.9257 (t) cc_final: 0.9045 (m) REVERT: C 377 ASN cc_start: 0.9203 (t0) cc_final: 0.8777 (t0) REVERT: C 395 TRP cc_start: 0.7546 (m100) cc_final: 0.7315 (m100) REVERT: C 475 MET cc_start: 0.8479 (mmm) cc_final: 0.7969 (mmm) REVERT: D 542 ARG cc_start: 0.8524 (ttp80) cc_final: 0.7979 (tpt170) REVERT: D 565 LEU cc_start: 0.7676 (tp) cc_final: 0.7318 (tp) REVERT: D 571 TRP cc_start: 0.7092 (t60) cc_final: 0.6856 (t60) REVERT: D 577 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7836 (tm-30) REVERT: D 585 ARG cc_start: 0.8526 (mmt180) cc_final: 0.8201 (ttm-80) REVERT: E 103 GLN cc_start: 0.8207 (tt0) cc_final: 0.7913 (tm-30) REVERT: E 434 MET cc_start: 0.8912 (ttp) cc_final: 0.8712 (ttp) REVERT: F 535 MET cc_start: 0.7831 (mpp) cc_final: 0.7617 (mpp) REVERT: F 536 THR cc_start: 0.8122 (p) cc_final: 0.7895 (p) REVERT: F 607 ASN cc_start: 0.8843 (p0) cc_final: 0.8423 (p0) REVERT: F 629 LEU cc_start: 0.8681 (tp) cc_final: 0.8397 (tp) REVERT: F 631 TRP cc_start: 0.8167 (t60) cc_final: 0.7770 (t-100) REVERT: F 634 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8093 (mm-30) REVERT: F 648 GLU cc_start: 0.8364 (tp30) cc_final: 0.8103 (tp30) outliers start: 2 outliers final: 0 residues processed: 319 average time/residue: 0.1232 time to fit residues: 58.3961 Evaluate side-chains 235 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.091853 restraints weight = 35823.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094484 restraints weight = 21277.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096282 restraints weight = 14983.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097495 restraints weight = 11778.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098197 restraints weight = 9949.247| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16194 Z= 0.144 Angle : 0.684 11.940 22182 Z= 0.328 Chirality : 0.047 0.442 2773 Planarity : 0.003 0.040 2679 Dihedral : 7.865 66.508 3805 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % Rotamer: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % 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: 0.96 (0.20), residues: 1678 helix: 1.93 (0.25), residues: 428 sheet: 0.72 (0.23), residues: 438 loop : -0.05 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 588 TYR 0.025 0.002 TYR D 643 PHE 0.017 0.002 PHE C 210 TRP 0.034 0.002 TRP C 69 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00319 (16072) covalent geometry : angle 0.63241 (21852) SS BOND : bond 0.00286 ( 36) SS BOND : angle 1.41706 ( 72) hydrogen bonds : bond 0.04550 ( 650) hydrogen bonds : angle 5.44929 ( 1797) link_ALPHA1-2 : bond 0.00930 ( 2) link_ALPHA1-2 : angle 1.81580 ( 6) link_ALPHA1-3 : bond 0.01273 ( 4) link_ALPHA1-3 : angle 1.85322 ( 12) link_ALPHA1-6 : bond 0.01218 ( 4) link_ALPHA1-6 : angle 1.38048 ( 12) link_BETA1-4 : bond 0.00588 ( 11) link_BETA1-4 : angle 1.88103 ( 33) link_NAG-ASN : bond 0.00376 ( 65) link_NAG-ASN : angle 2.58394 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 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 104 MET cc_start: 0.8913 (tpp) cc_final: 0.8545 (tpp) REVERT: A 209 SER cc_start: 0.8713 (t) cc_final: 0.8436 (p) REVERT: A 256 SER cc_start: 0.9463 (p) cc_final: 0.8973 (m) REVERT: B 599 SER cc_start: 0.8908 (p) cc_final: 0.8216 (t) REVERT: B 634 GLU cc_start: 0.8166 (pt0) cc_final: 0.7492 (pp20) REVERT: B 641 ILE cc_start: 0.8044 (mp) cc_final: 0.7353 (tp) REVERT: B 643 TYR cc_start: 0.9000 (m-10) cc_final: 0.8682 (m-10) REVERT: C 114 GLN cc_start: 0.8594 (tp40) cc_final: 0.7588 (tm-30) REVERT: C 199 SER cc_start: 0.9448 (p) cc_final: 0.9154 (t) REVERT: C 377 ASN cc_start: 0.9259 (t0) cc_final: 0.8775 (t0) REVERT: C 414 ILE cc_start: 0.9317 (mm) cc_final: 0.9101 (tp) REVERT: D 567 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8621 (tmtt) REVERT: D 585 ARG cc_start: 0.8504 (mmt180) cc_final: 0.8180 (ttm-80) REVERT: D 586 TYR cc_start: 0.9325 (t80) cc_final: 0.8991 (t80) REVERT: D 588 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8466 (tmm-80) REVERT: D 601 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8807 (ptpp) REVERT: D 615 SER cc_start: 0.8246 (t) cc_final: 0.7956 (m) REVERT: D 650 GLN cc_start: 0.8750 (tp40) cc_final: 0.7908 (tm-30) REVERT: E 103 GLN cc_start: 0.8108 (tt0) cc_final: 0.7761 (tm-30) REVERT: E 150 MET cc_start: 0.7981 (mmm) cc_final: 0.7457 (mmt) REVERT: E 381 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6982 (tt0) REVERT: F 607 ASN cc_start: 0.8867 (p0) cc_final: 0.8387 (p0) REVERT: F 634 GLU cc_start: 0.8760 (mt-10) cc_final: 0.7965 (mm-30) REVERT: F 648 GLU cc_start: 0.8352 (tp30) cc_final: 0.8118 (tp30) outliers start: 2 outliers final: 0 residues processed: 304 average time/residue: 0.1225 time to fit residues: 55.8116 Evaluate side-chains 236 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 562 GLN C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085753 restraints weight = 36404.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088078 restraints weight = 22323.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089707 restraints weight = 16162.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090777 restraints weight = 12890.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091526 restraints weight = 11057.795| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 16194 Z= 0.272 Angle : 0.809 16.191 22182 Z= 0.386 Chirality : 0.050 0.427 2773 Planarity : 0.004 0.048 2679 Dihedral : 7.826 61.416 3805 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.58 % 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: 0.64 (0.20), residues: 1678 helix: 1.63 (0.25), residues: 431 sheet: 0.56 (0.24), residues: 429 loop : -0.23 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 151 TYR 0.017 0.002 TYR E 173 PHE 0.019 0.003 PHE A 361 TRP 0.041 0.002 TRP C 69 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00631 (16072) covalent geometry : angle 0.74737 (21852) SS BOND : bond 0.00484 ( 36) SS BOND : angle 1.69188 ( 72) hydrogen bonds : bond 0.05105 ( 650) hydrogen bonds : angle 5.54196 ( 1797) link_ALPHA1-2 : bond 0.00589 ( 2) link_ALPHA1-2 : angle 2.08121 ( 6) link_ALPHA1-3 : bond 0.01091 ( 4) link_ALPHA1-3 : angle 2.15637 ( 12) link_ALPHA1-6 : bond 0.01367 ( 4) link_ALPHA1-6 : angle 1.63528 ( 12) link_BETA1-4 : bond 0.00438 ( 11) link_BETA1-4 : angle 1.93168 ( 33) link_NAG-ASN : bond 0.00490 ( 65) link_NAG-ASN : angle 3.08998 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 VAL cc_start: 0.9376 (m) cc_final: 0.9110 (p) REVERT: A 209 SER cc_start: 0.8880 (t) cc_final: 0.8648 (p) REVERT: A 217 TYR cc_start: 0.8519 (m-10) cc_final: 0.8175 (m-10) REVERT: A 256 SER cc_start: 0.9487 (p) cc_final: 0.9056 (m) REVERT: A 315 GLN cc_start: 0.8489 (mp10) cc_final: 0.8274 (mp10) REVERT: A 475 MET cc_start: 0.8874 (mmm) cc_final: 0.8674 (tpp) REVERT: B 599 SER cc_start: 0.9050 (p) cc_final: 0.8408 (t) REVERT: B 601 LYS cc_start: 0.8681 (tptt) cc_final: 0.8357 (tppt) REVERT: B 634 GLU cc_start: 0.8169 (pt0) cc_final: 0.7429 (pp20) REVERT: B 641 ILE cc_start: 0.8168 (mp) cc_final: 0.7781 (tp) REVERT: B 643 TYR cc_start: 0.9055 (m-10) cc_final: 0.8699 (m-10) REVERT: C 38 VAL cc_start: 0.8286 (t) cc_final: 0.7934 (t) REVERT: C 150 MET cc_start: 0.8775 (ppp) cc_final: 0.7805 (ppp) REVERT: C 199 SER cc_start: 0.9485 (p) cc_final: 0.9194 (t) REVERT: C 414 ILE cc_start: 0.9418 (mm) cc_final: 0.9207 (tp) REVERT: C 475 MET cc_start: 0.8722 (mmm) cc_final: 0.8154 (mmm) REVERT: D 565 LEU cc_start: 0.8055 (tp) cc_final: 0.7420 (tp) REVERT: D 571 TRP cc_start: 0.7302 (t60) cc_final: 0.6831 (t60) REVERT: D 585 ARG cc_start: 0.8609 (mmt180) cc_final: 0.8206 (ttm-80) REVERT: D 588 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8527 (ttp80) REVERT: D 601 LYS cc_start: 0.9244 (ptpt) cc_final: 0.8931 (ptpp) REVERT: D 615 SER cc_start: 0.8250 (t) cc_final: 0.7917 (m) REVERT: E 103 GLN cc_start: 0.8474 (tt0) cc_final: 0.7988 (tm-30) REVERT: E 150 MET cc_start: 0.8057 (mmm) cc_final: 0.7652 (mmt) REVERT: E 381 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7065 (tt0) REVERT: F 607 ASN cc_start: 0.9033 (p0) cc_final: 0.8507 (p0) REVERT: F 634 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7965 (mm-30) REVERT: F 648 GLU cc_start: 0.8527 (tp30) cc_final: 0.8246 (tp30) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.1260 time to fit residues: 52.8207 Evaluate side-chains 218 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 71 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087942 restraints weight = 35696.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090361 restraints weight = 21809.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092008 restraints weight = 15640.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093116 restraints weight = 12443.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093753 restraints weight = 10626.123| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16194 Z= 0.156 Angle : 0.713 13.572 22182 Z= 0.338 Chirality : 0.048 0.471 2773 Planarity : 0.004 0.042 2679 Dihedral : 7.343 59.131 3805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 0.66 (0.20), residues: 1678 helix: 1.80 (0.26), residues: 432 sheet: 0.55 (0.24), residues: 425 loop : -0.32 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 588 TYR 0.016 0.002 TYR E 173 PHE 0.014 0.002 PHE A 383 TRP 0.047 0.002 TRP C 69 HIS 0.004 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00355 (16072) covalent geometry : angle 0.64707 (21852) SS BOND : bond 0.00342 ( 36) SS BOND : angle 1.53944 ( 72) hydrogen bonds : bond 0.04522 ( 650) hydrogen bonds : angle 5.33715 ( 1797) link_ALPHA1-2 : bond 0.00700 ( 2) link_ALPHA1-2 : angle 1.83393 ( 6) link_ALPHA1-3 : bond 0.01238 ( 4) link_ALPHA1-3 : angle 2.01268 ( 12) link_ALPHA1-6 : bond 0.01448 ( 4) link_ALPHA1-6 : angle 1.90080 ( 12) link_BETA1-4 : bond 0.00483 ( 11) link_BETA1-4 : angle 1.50243 ( 33) link_NAG-ASN : bond 0.00378 ( 65) link_NAG-ASN : angle 3.00495 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9134 (tpp) cc_final: 0.8774 (tpp) REVERT: A 202 THR cc_start: 0.9564 (m) cc_final: 0.9206 (p) REVERT: A 256 SER cc_start: 0.9429 (p) cc_final: 0.9093 (m) REVERT: A 315 GLN cc_start: 0.8495 (mp10) cc_final: 0.8154 (mp10) REVERT: B 599 SER cc_start: 0.8925 (p) cc_final: 0.8372 (t) REVERT: B 601 LYS cc_start: 0.8564 (tptt) cc_final: 0.8278 (tppt) REVERT: B 634 GLU cc_start: 0.7753 (pt0) cc_final: 0.7329 (pp20) REVERT: B 641 ILE cc_start: 0.8124 (mp) cc_final: 0.7492 (tp) REVERT: C 38 VAL cc_start: 0.8148 (t) cc_final: 0.7847 (t) REVERT: C 150 MET cc_start: 0.8517 (ppp) cc_final: 0.7542 (ppp) REVERT: C 199 SER cc_start: 0.9406 (p) cc_final: 0.9100 (t) REVERT: C 414 ILE cc_start: 0.9379 (mm) cc_final: 0.9172 (tp) REVERT: C 475 MET cc_start: 0.8698 (mmm) cc_final: 0.8194 (mmm) REVERT: D 577 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7920 (tm-30) REVERT: D 585 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8132 (ttm-80) REVERT: D 588 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8551 (ttp80) REVERT: E 103 GLN cc_start: 0.8396 (tt0) cc_final: 0.7839 (tm-30) REVERT: E 150 MET cc_start: 0.8039 (mmm) cc_final: 0.7672 (mmt) REVERT: E 381 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7109 (tt0) REVERT: F 607 ASN cc_start: 0.8986 (p0) cc_final: 0.8407 (p0) REVERT: F 634 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7855 (mm-30) REVERT: F 648 GLU cc_start: 0.8414 (tp30) cc_final: 0.8178 (tp30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1224 time to fit residues: 50.8910 Evaluate side-chains 222 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 149 optimal weight: 0.0070 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN C 352 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087716 restraints weight = 35560.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090117 restraints weight = 21459.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.091716 restraints weight = 15244.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092834 restraints weight = 12072.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093401 restraints weight = 10249.261| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16194 Z= 0.154 Angle : 0.707 16.458 22182 Z= 0.336 Chirality : 0.050 0.762 2773 Planarity : 0.004 0.046 2679 Dihedral : 7.179 56.273 3805 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 0.07 % Allowed : 1.05 % Favored : 98.89 % 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: 0.61 (0.20), residues: 1678 helix: 1.74 (0.26), residues: 428 sheet: 0.60 (0.24), residues: 437 loop : -0.39 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 588 TYR 0.016 0.002 TYR E 173 PHE 0.013 0.002 PHE A 210 TRP 0.053 0.002 TRP C 69 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00347 (16072) covalent geometry : angle 0.64885 (21852) SS BOND : bond 0.00384 ( 36) SS BOND : angle 1.53238 ( 72) hydrogen bonds : bond 0.04460 ( 650) hydrogen bonds : angle 5.24721 ( 1797) link_ALPHA1-2 : bond 0.00634 ( 2) link_ALPHA1-2 : angle 1.82142 ( 6) link_ALPHA1-3 : bond 0.01263 ( 4) link_ALPHA1-3 : angle 2.03951 ( 12) link_ALPHA1-6 : bond 0.01441 ( 4) link_ALPHA1-6 : angle 1.92123 ( 12) link_BETA1-4 : bond 0.00464 ( 11) link_BETA1-4 : angle 1.40421 ( 33) link_NAG-ASN : bond 0.00437 ( 65) link_NAG-ASN : angle 2.80693 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.9057 (m) cc_final: 0.8764 (p) REVERT: A 202 THR cc_start: 0.9544 (m) cc_final: 0.9131 (p) REVERT: A 217 TYR cc_start: 0.8395 (m-10) cc_final: 0.7856 (m-10) REVERT: A 256 SER cc_start: 0.9397 (p) cc_final: 0.9097 (m) REVERT: A 315 GLN cc_start: 0.8492 (mp10) cc_final: 0.8270 (mp10) REVERT: B 560 GLU cc_start: 0.7815 (mp0) cc_final: 0.7521 (mm-30) REVERT: B 584 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 599 SER cc_start: 0.8918 (p) cc_final: 0.8387 (t) REVERT: B 634 GLU cc_start: 0.8068 (pt0) cc_final: 0.7512 (pp20) REVERT: B 641 ILE cc_start: 0.8147 (mp) cc_final: 0.7555 (tp) REVERT: B 643 TYR cc_start: 0.9091 (m-10) cc_final: 0.8737 (m-10) REVERT: C 38 VAL cc_start: 0.8156 (t) cc_final: 0.7794 (t) REVERT: C 150 MET cc_start: 0.8536 (ppp) cc_final: 0.7498 (ppp) REVERT: C 199 SER cc_start: 0.9443 (p) cc_final: 0.9135 (t) REVERT: C 210 PHE cc_start: 0.7915 (m-80) cc_final: 0.7008 (m-80) REVERT: C 295 ASN cc_start: 0.8375 (m-40) cc_final: 0.8163 (m-40) REVERT: C 369 LEU cc_start: 0.8028 (mp) cc_final: 0.7807 (tp) REVERT: D 530 MET cc_start: 0.8282 (ttm) cc_final: 0.8072 (ttt) REVERT: D 577 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 585 ARG cc_start: 0.8558 (mmt180) cc_final: 0.8179 (ttm-80) REVERT: E 95 MET cc_start: 0.8880 (ppp) cc_final: 0.8676 (ppp) REVERT: E 103 GLN cc_start: 0.8224 (tt0) cc_final: 0.7820 (tm-30) REVERT: E 150 MET cc_start: 0.8022 (mmm) cc_final: 0.7712 (mmt) REVERT: E 381 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6972 (tt0) REVERT: E 500 ARG cc_start: 0.5791 (mtt180) cc_final: 0.4948 (pmt170) REVERT: F 607 ASN cc_start: 0.8996 (p0) cc_final: 0.8407 (p0) REVERT: F 634 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7805 (mm-30) outliers start: 1 outliers final: 1 residues processed: 284 average time/residue: 0.1159 time to fit residues: 49.3550 Evaluate side-chains 223 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 114 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088367 restraints weight = 36019.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090645 restraints weight = 21977.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092246 restraints weight = 15851.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093305 restraints weight = 12594.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094013 restraints weight = 10750.851| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16194 Z= 0.144 Angle : 0.698 16.275 22182 Z= 0.333 Chirality : 0.048 0.502 2773 Planarity : 0.004 0.049 2679 Dihedral : 6.993 56.067 3805 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.57 (0.20), residues: 1678 helix: 1.81 (0.26), residues: 422 sheet: 0.56 (0.25), residues: 432 loop : -0.44 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 500 TYR 0.020 0.002 TYR A 217 PHE 0.013 0.002 PHE A 383 TRP 0.071 0.002 TRP D 610 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00325 (16072) covalent geometry : angle 0.64304 (21852) SS BOND : bond 0.00406 ( 36) SS BOND : angle 1.54063 ( 72) hydrogen bonds : bond 0.04294 ( 650) hydrogen bonds : angle 5.16197 ( 1797) link_ALPHA1-2 : bond 0.00624 ( 2) link_ALPHA1-2 : angle 1.80515 ( 6) link_ALPHA1-3 : bond 0.01143 ( 4) link_ALPHA1-3 : angle 1.94868 ( 12) link_ALPHA1-6 : bond 0.01415 ( 4) link_ALPHA1-6 : angle 1.97355 ( 12) link_BETA1-4 : bond 0.00475 ( 11) link_BETA1-4 : angle 1.31172 ( 33) link_NAG-ASN : bond 0.00501 ( 65) link_NAG-ASN : angle 2.70888 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.9102 (m) cc_final: 0.8737 (p) REVERT: A 104 MET cc_start: 0.9195 (tpp) cc_final: 0.8733 (tpp) REVERT: A 202 THR cc_start: 0.9503 (m) cc_final: 0.9095 (p) REVERT: A 256 SER cc_start: 0.9356 (p) cc_final: 0.9091 (m) REVERT: A 315 GLN cc_start: 0.8506 (mp10) cc_final: 0.8234 (mp10) REVERT: B 599 SER cc_start: 0.8890 (p) cc_final: 0.8379 (t) REVERT: B 628 TRP cc_start: 0.7761 (m100) cc_final: 0.7557 (m100) REVERT: B 634 GLU cc_start: 0.7959 (pt0) cc_final: 0.7501 (pp20) REVERT: B 641 ILE cc_start: 0.8090 (mp) cc_final: 0.7502 (tp) REVERT: C 38 VAL cc_start: 0.8026 (t) cc_final: 0.7609 (t) REVERT: C 114 GLN cc_start: 0.8681 (tp40) cc_final: 0.7742 (tm-30) REVERT: C 150 MET cc_start: 0.8568 (ppp) cc_final: 0.7494 (ppp) REVERT: C 199 SER cc_start: 0.9400 (p) cc_final: 0.9072 (t) REVERT: C 295 ASN cc_start: 0.8280 (m-40) cc_final: 0.8075 (m-40) REVERT: C 369 LEU cc_start: 0.8150 (mp) cc_final: 0.7848 (tp) REVERT: D 577 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 596 TRP cc_start: 0.7943 (m-10) cc_final: 0.7654 (m-10) REVERT: D 610 TRP cc_start: 0.7500 (t60) cc_final: 0.7165 (t60) REVERT: E 95 MET cc_start: 0.8872 (ppp) cc_final: 0.8658 (ppp) REVERT: E 103 GLN cc_start: 0.8193 (tt0) cc_final: 0.7822 (tm-30) REVERT: E 150 MET cc_start: 0.8000 (mmm) cc_final: 0.7718 (mmt) REVERT: E 381 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7256 (tt0) REVERT: E 500 ARG cc_start: 0.5858 (mtt180) cc_final: 0.5022 (pmt170) REVERT: F 607 ASN cc_start: 0.9011 (p0) cc_final: 0.8403 (p0) REVERT: F 626 MET cc_start: 0.7309 (ttm) cc_final: 0.7054 (ttm) REVERT: F 634 GLU cc_start: 0.8673 (mt-10) cc_final: 0.7764 (mm-30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1200 time to fit residues: 49.1552 Evaluate side-chains 222 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 65 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS D 575 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086731 restraints weight = 36137.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088846 restraints weight = 22925.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090151 restraints weight = 16850.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091231 restraints weight = 13758.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.091827 restraints weight = 11828.010| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16194 Z= 0.203 Angle : 0.761 15.938 22182 Z= 0.367 Chirality : 0.050 0.458 2773 Planarity : 0.004 0.054 2679 Dihedral : 7.183 57.601 3805 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 0.37 (0.20), residues: 1678 helix: 1.62 (0.26), residues: 426 sheet: 0.51 (0.24), residues: 446 loop : -0.63 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 588 TYR 0.021 0.002 TYR A 173 PHE 0.015 0.002 PHE A 361 TRP 0.051 0.003 TRP C 69 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00467 (16072) covalent geometry : angle 0.70694 (21852) SS BOND : bond 0.00420 ( 36) SS BOND : angle 1.57197 ( 72) hydrogen bonds : bond 0.04817 ( 650) hydrogen bonds : angle 5.29629 ( 1797) link_ALPHA1-2 : bond 0.00469 ( 2) link_ALPHA1-2 : angle 1.91437 ( 6) link_ALPHA1-3 : bond 0.01029 ( 4) link_ALPHA1-3 : angle 2.11301 ( 12) link_ALPHA1-6 : bond 0.01411 ( 4) link_ALPHA1-6 : angle 2.22266 ( 12) link_BETA1-4 : bond 0.00399 ( 11) link_BETA1-4 : angle 1.41692 ( 33) link_NAG-ASN : bond 0.00479 ( 65) link_NAG-ASN : angle 2.82249 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9046 (tpp) cc_final: 0.8748 (tpt) REVERT: A 202 THR cc_start: 0.9513 (m) cc_final: 0.9211 (p) REVERT: A 256 SER cc_start: 0.9373 (p) cc_final: 0.9059 (m) REVERT: A 315 GLN cc_start: 0.8629 (mp10) cc_final: 0.8275 (mp10) REVERT: B 599 SER cc_start: 0.8905 (p) cc_final: 0.8440 (t) REVERT: B 634 GLU cc_start: 0.7883 (pt0) cc_final: 0.7514 (pp20) REVERT: B 641 ILE cc_start: 0.8064 (mp) cc_final: 0.7679 (tp) REVERT: C 38 VAL cc_start: 0.8051 (t) cc_final: 0.7776 (t) REVERT: C 199 SER cc_start: 0.9311 (p) cc_final: 0.9052 (t) REVERT: D 577 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7848 (tm-30) REVERT: E 95 MET cc_start: 0.8872 (ppp) cc_final: 0.8557 (ppp) REVERT: E 103 GLN cc_start: 0.8280 (tt0) cc_final: 0.8057 (tm-30) REVERT: E 150 MET cc_start: 0.7938 (mmm) cc_final: 0.7647 (mmt) REVERT: E 500 ARG cc_start: 0.5913 (mtt180) cc_final: 0.5170 (pmt170) REVERT: F 607 ASN cc_start: 0.9052 (p0) cc_final: 0.8353 (p0) REVERT: F 634 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7601 (mm-30) REVERT: F 654 GLU cc_start: 0.9065 (tp30) cc_final: 0.8782 (tp30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1175 time to fit residues: 46.8772 Evaluate side-chains 205 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 170 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 563 GLN D 575 GLN E 195 ASN E 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088227 restraints weight = 35461.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.090643 restraints weight = 21340.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092259 restraints weight = 15111.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093267 restraints weight = 11942.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094087 restraints weight = 10218.649| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16194 Z= 0.146 Angle : 0.732 21.047 22182 Z= 0.348 Chirality : 0.049 0.569 2773 Planarity : 0.004 0.055 2679 Dihedral : 6.923 56.139 3805 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.39 (0.20), residues: 1678 helix: 1.69 (0.26), residues: 426 sheet: 0.57 (0.25), residues: 434 loop : -0.67 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 588 TYR 0.030 0.002 TYR D 643 PHE 0.012 0.002 PHE A 383 TRP 0.094 0.003 TRP D 614 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00332 (16072) covalent geometry : angle 0.65704 (21852) SS BOND : bond 0.00361 ( 36) SS BOND : angle 1.41153 ( 72) hydrogen bonds : bond 0.04457 ( 650) hydrogen bonds : angle 5.14601 ( 1797) link_ALPHA1-2 : bond 0.00594 ( 2) link_ALPHA1-2 : angle 1.78564 ( 6) link_ALPHA1-3 : bond 0.01080 ( 4) link_ALPHA1-3 : angle 1.95072 ( 12) link_ALPHA1-6 : bond 0.01401 ( 4) link_ALPHA1-6 : angle 2.29502 ( 12) link_BETA1-4 : bond 0.00461 ( 11) link_BETA1-4 : angle 1.23041 ( 33) link_NAG-ASN : bond 0.00447 ( 65) link_NAG-ASN : angle 3.30622 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9070 (tpp) cc_final: 0.8835 (tpt) REVERT: A 178 ARG cc_start: 0.8084 (tpt90) cc_final: 0.7844 (tpt90) REVERT: A 202 THR cc_start: 0.9453 (m) cc_final: 0.9121 (p) REVERT: A 256 SER cc_start: 0.9355 (p) cc_final: 0.9103 (m) REVERT: A 315 GLN cc_start: 0.8561 (mp10) cc_final: 0.8258 (mp10) REVERT: B 535 MET cc_start: 0.7603 (mpp) cc_final: 0.7340 (mmt) REVERT: B 634 GLU cc_start: 0.7990 (pt0) cc_final: 0.7496 (pp20) REVERT: B 641 ILE cc_start: 0.8096 (mp) cc_final: 0.7514 (tp) REVERT: B 648 GLU cc_start: 0.8003 (tp30) cc_final: 0.7798 (tp30) REVERT: C 114 GLN cc_start: 0.8729 (tp40) cc_final: 0.7776 (tm-30) REVERT: C 150 MET cc_start: 0.8754 (ppp) cc_final: 0.7618 (ppp) REVERT: C 199 SER cc_start: 0.9345 (p) cc_final: 0.9076 (t) REVERT: C 210 PHE cc_start: 0.8124 (m-80) cc_final: 0.7433 (m-80) REVERT: D 577 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 95 MET cc_start: 0.8852 (ppp) cc_final: 0.8509 (ppp) REVERT: E 103 GLN cc_start: 0.8180 (tt0) cc_final: 0.7841 (tm-30) REVERT: E 500 ARG cc_start: 0.5914 (mtt180) cc_final: 0.5051 (pmt170) REVERT: F 607 ASN cc_start: 0.8984 (p0) cc_final: 0.8316 (p0) REVERT: F 634 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7588 (mm-30) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1231 time to fit residues: 49.7383 Evaluate side-chains 220 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 GLN E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088518 restraints weight = 35819.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090932 restraints weight = 21538.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092558 restraints weight = 15295.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093632 restraints weight = 12103.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094407 restraints weight = 10309.901| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16194 Z= 0.144 Angle : 0.724 19.367 22182 Z= 0.343 Chirality : 0.048 0.521 2773 Planarity : 0.004 0.055 2679 Dihedral : 6.762 57.969 3805 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.39 (0.20), residues: 1678 helix: 1.70 (0.26), residues: 426 sheet: 0.52 (0.25), residues: 438 loop : -0.65 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 585 TYR 0.020 0.002 TYR A 217 PHE 0.012 0.001 PHE A 383 TRP 0.086 0.003 TRP D 614 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00327 (16072) covalent geometry : angle 0.65830 (21852) SS BOND : bond 0.00351 ( 36) SS BOND : angle 1.41166 ( 72) hydrogen bonds : bond 0.04389 ( 650) hydrogen bonds : angle 5.13867 ( 1797) link_ALPHA1-2 : bond 0.00585 ( 2) link_ALPHA1-2 : angle 1.78678 ( 6) link_ALPHA1-3 : bond 0.01092 ( 4) link_ALPHA1-3 : angle 1.96591 ( 12) link_ALPHA1-6 : bond 0.01422 ( 4) link_ALPHA1-6 : angle 2.43065 ( 12) link_BETA1-4 : bond 0.00475 ( 11) link_BETA1-4 : angle 1.27684 ( 33) link_NAG-ASN : bond 0.00432 ( 65) link_NAG-ASN : angle 3.05743 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.59 seconds wall clock time: 40 minutes 26.08 seconds (2426.08 seconds total)