Starting phenix.real_space_refine on Wed Mar 4 20:32:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t73_25732/03_2026/7t73_25732.map" } resolution = 4.0 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= 0.001 sd= 0.120 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 107 5.16 5 C 9994 2.51 5 N 2660 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16010 Number of models: 1 Model: "" Number of chains: 28 Chain: "H" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1046 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3392 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 2 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3458 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 23, 'TRANS': 417} Chain breaks: 2 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 934 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "U" 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: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: "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: 4.04, per 1000 atoms: 0.25 Number of scatterers: 16010 At special positions: 0 Unit cell: (129.95, 128.8, 156.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 3249 8.00 N 2660 7.00 C 9994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.19 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 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=2.17 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=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.18 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=2.23 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.14 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 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=2.09 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 D 598 " - pdb=" SG CYS D 604 " distance=2.02 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 7 " " MAN V 4 " - " MAN V 5 " ALPHA1-6 " BMA V 3 " - " MAN V 4 " " MAN V 4 " - " MAN V 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 301 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 332 " " NAG A 608 " - " ASN A 355 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E1001 " - " ASN E 197 " " NAG E1002 " - " ASN E 301 " " NAG E1003 " - " ASN E 448 " " NAG E1004 " - " ASN E 276 " " NAG E1005 " - " ASN E 392 " " NAG E1006 " - " ASN E 88 " " NAG E1007 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN E 156 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 332 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN E 160 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 669.3 milliseconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3538 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 30 sheets defined 23.3% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.187A 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 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.273A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.516A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.597A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 660 removed outlier: 4.509A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.906A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 460 through 464 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.898A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.147A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 341 through 353 removed outlier: 3.824A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.712A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.120A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.762A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 639 through 650 Processing helix chain 'D' and resid 651 through 653 No H-bonds generated for 'chain 'D' and resid 651 through 653' Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.276A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.977A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 620 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.295A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 660 removed outlier: 4.219A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.822A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.695A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 40 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.469A pdb=" N VAL A 242 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 87 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.665A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.869A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 132 removed outlier: 4.231A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.523A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 466 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB4, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.305A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.752A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C 86 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.601A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 202 removed outlier: 6.359A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 283 through 298 removed outlier: 6.923A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AC3, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.545A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.520A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.532A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 3.702A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD3, first strand: chain 'E' and resid 423 through 424 401 hydrogen bonds defined for protein. 1029 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: 2.54 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.32: 3006 1.32 - 1.49: 6620 1.49 - 1.66: 6556 1.66 - 1.83: 107 1.83 - 2.00: 34 Bond restraints: 16323 Sorted by residual: bond pdb=" CA SER E 174 " pdb=" CB SER E 174 " ideal model delta sigma weight residual 1.533 1.377 0.156 1.60e-02 3.91e+03 9.47e+01 bond pdb=" CA SER E 158 " pdb=" CB SER E 158 " ideal model delta sigma weight residual 1.532 1.388 0.144 1.58e-02 4.01e+03 8.31e+01 bond pdb=" C LEU E 175 " pdb=" O LEU E 175 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.21e-02 6.83e+03 5.53e+01 bond pdb=" CB ILE L 106 " pdb=" CG1 ILE L 106 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C SER E 158 " pdb=" O SER E 158 " ideal model delta sigma weight residual 1.235 1.158 0.078 1.12e-02 7.97e+03 4.80e+01 ... (remaining 16318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.61: 22106 7.61 - 15.22: 69 15.22 - 22.83: 1 22.83 - 30.44: 0 30.44 - 38.05: 4 Bond angle restraints: 22180 Sorted by residual: angle pdb=" C ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta sigma weight residual 110.22 88.52 21.70 1.67e+00 3.59e-01 1.69e+02 angle pdb=" C2 NAG U 1 " pdb=" N2 NAG U 1 " pdb=" C7 NAG U 1 " ideal model delta sigma weight residual 124.56 162.61 -38.05 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG A 609 " pdb=" N2 NAG A 609 " pdb=" C7 NAG A 609 " ideal model delta sigma weight residual 124.56 161.28 -36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 160.09 -35.53 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 603 " pdb=" N2 NAG A 603 " pdb=" C7 NAG A 603 " ideal model delta sigma weight residual 124.56 158.89 -34.33 3.00e+00 1.11e-01 1.31e+02 ... (remaining 22175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 10343 21.90 - 43.80: 288 43.80 - 65.70: 93 65.70 - 87.60: 48 87.60 - 109.50: 28 Dihedral angle restraints: 10800 sinusoidal: 5313 harmonic: 5487 Sorted by residual: dihedral pdb=" C ASN E 156 " pdb=" N ASN E 156 " pdb=" CA ASN E 156 " pdb=" CB ASN E 156 " ideal model delta harmonic sigma weight residual -122.60 -93.57 -29.03 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 2578 0.307 - 0.614: 140 0.614 - 0.922: 1 0.922 - 1.229: 0 1.229 - 1.536: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 4.99e+02 chirality pdb=" C1 MAN V 6 " pdb=" O6 MAN V 4 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.60e+02 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 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 2717 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.372 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C7 NAG N 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.561 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 703 " -0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG D 703 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D 703 " -0.149 2.00e-02 2.50e+03 pdb=" N2 NAG D 703 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG D 703 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " 0.339 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG B 701 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " 0.056 2.00e-02 2.50e+03 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 1 2.20 - 2.87: 5544 2.87 - 3.55: 20487 3.55 - 4.22: 38529 4.22 - 4.90: 59536 Nonbonded interactions: 124097 Sorted by model distance: nonbonded pdb=" OG SER F 613 " pdb=" C1 NAG F 701 " model vdw 1.521 3.470 nonbonded pdb=" O5 NAG B 702 " pdb=" O6 NAG B 702 " model vdw 2.217 2.432 nonbonded pdb=" OG SER F 613 " pdb=" O5 NAG F 701 " model vdw 2.244 3.040 nonbonded pdb=" O5 NAG N 1 " pdb=" O6 NAG N 1 " model vdw 2.262 2.432 nonbonded pdb=" O ASN E 136 " pdb=" CB ASN E 136 " model vdw 2.268 2.752 ... (remaining 124092 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 32 through 57 or resid 74 through 607)) selection = (chain 'C' and resid 32 through 607) selection = (chain 'E' and (resid 32 through 57 or resid 74 through 1007)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.410 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 0.198 16435 Z= 1.158 Angle : 1.956 38.047 22482 Z= 1.222 Chirality : 0.145 1.536 2720 Planarity : 0.018 0.317 2735 Dihedral : 13.611 109.497 7160 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.80 % Allowed : 3.48 % Favored : 95.72 % Rotamer: Outliers : 1.56 % Allowed : 1.38 % Favored : 97.07 % Cbeta Deviations : 0.79 % 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: -0.60 (0.18), residues: 1867 helix: -1.13 (0.24), residues: 355 sheet: -0.07 (0.23), residues: 477 loop : -0.16 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 169 TYR 0.048 0.007 TYR C 191 PHE 0.062 0.006 PHE E 159 TRP 0.068 0.009 TRP E 479 HIS 0.011 0.002 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.02102 (16323) covalent geometry : angle 1.92053 (22180) SS BOND : bond 0.06003 ( 34) SS BOND : angle 3.55281 ( 68) hydrogen bonds : bond 0.18662 ( 401) hydrogen bonds : angle 7.61903 ( 1029) link_ALPHA1-3 : bond 0.06745 ( 5) link_ALPHA1-3 : angle 4.43189 ( 15) link_ALPHA1-6 : bond 0.00309 ( 2) link_ALPHA1-6 : angle 3.23323 ( 6) link_BETA1-4 : bond 0.06089 ( 20) link_BETA1-4 : angle 4.91008 ( 60) link_NAG-ASN : bond 0.07278 ( 51) link_NAG-ASN : angle 3.21048 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 503 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.7273 (p0) cc_final: 0.7034 (p0) REVERT: H 107 THR cc_start: 0.3110 (t) cc_final: 0.2350 (m) REVERT: L 48 ILE cc_start: 0.7032 (mt) cc_final: 0.6825 (tt) REVERT: A 35 TRP cc_start: 0.8285 (m100) cc_final: 0.7595 (m-10) REVERT: A 104 MET cc_start: 0.9451 (ttt) cc_final: 0.9189 (ttp) REVERT: A 287 GLN cc_start: 0.7552 (tt0) cc_final: 0.7110 (mm110) REVERT: A 426 MET cc_start: 0.7700 (ttt) cc_final: 0.7232 (tpt) REVERT: B 626 MET cc_start: 0.7680 (mtp) cc_final: 0.7475 (mtt) REVERT: B 632 ASP cc_start: 0.8720 (t70) cc_final: 0.8423 (t70) REVERT: C 82 GLN cc_start: 0.7248 (mt0) cc_final: 0.7045 (tt0) REVERT: C 97 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7571 (tptp) REVERT: C 129 LEU cc_start: 0.9191 (mt) cc_final: 0.8965 (mp) REVERT: C 156 ASN cc_start: 0.9315 (t0) cc_final: 0.8821 (t0) REVERT: C 168 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7292 (mtmm) REVERT: C 492 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8323 (mt-10) REVERT: C 498 PRO cc_start: 0.9499 (OUTLIER) cc_final: 0.8849 (Cg_exo) REVERT: E 194 ILE cc_start: 0.8929 (tp) cc_final: 0.8427 (tt) REVERT: E 239 CYS cc_start: 0.8366 (t) cc_final: 0.8116 (t) REVERT: E 264 SER cc_start: 0.8447 (t) cc_final: 0.7802 (m) REVERT: E 282 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8948 (mmmt) REVERT: D 522 PHE cc_start: 0.9223 (t80) cc_final: 0.8951 (t80) REVERT: D 536 THR cc_start: 0.7947 (p) cc_final: 0.7437 (t) REVERT: D 610 TRP cc_start: 0.8843 (t-100) cc_final: 0.8384 (t-100) REVERT: D 623 TRP cc_start: 0.8951 (m100) cc_final: 0.8052 (m100) REVERT: D 643 TYR cc_start: 0.8532 (m-10) cc_final: 0.8273 (m-80) REVERT: F 543 ASN cc_start: 0.8597 (m-40) cc_final: 0.8225 (m-40) REVERT: F 601 LYS cc_start: 0.8900 (mttt) cc_final: 0.8667 (mmtp) outliers start: 26 outliers final: 8 residues processed: 520 average time/residue: 0.1382 time to fit residues: 105.3024 Evaluate side-chains 280 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 271 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 498 PRO Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain F residue 615 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 103 GLN A 170 GLN A 203 GLN B 591 GLN C 85 HIS C 234 ASN C 300 ASN C 363 GLN E 136 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127659 restraints weight = 23770.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127317 restraints weight = 25070.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129901 restraints weight = 23749.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130172 restraints weight = 16913.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130448 restraints weight = 16019.579| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16435 Z= 0.181 Angle : 0.847 10.035 22482 Z= 0.409 Chirality : 0.051 0.288 2720 Planarity : 0.004 0.033 2735 Dihedral : 11.153 87.263 3663 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.95 % Favored : 96.89 % Rotamer: Outliers : 2.99 % Allowed : 10.23 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.44 (0.19), residues: 1867 helix: 0.02 (0.29), residues: 339 sheet: 0.09 (0.23), residues: 479 loop : -0.52 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 542 TYR 0.025 0.002 TYR L 49 PHE 0.020 0.003 PHE C 353 TRP 0.031 0.003 TRP B 610 HIS 0.008 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00409 (16323) covalent geometry : angle 0.78739 (22180) SS BOND : bond 0.00664 ( 34) SS BOND : angle 2.10258 ( 68) hydrogen bonds : bond 0.06101 ( 401) hydrogen bonds : angle 5.85627 ( 1029) link_ALPHA1-3 : bond 0.01051 ( 5) link_ALPHA1-3 : angle 2.97633 ( 15) link_ALPHA1-6 : bond 0.01593 ( 2) link_ALPHA1-6 : angle 1.87703 ( 6) link_BETA1-4 : bond 0.00773 ( 20) link_BETA1-4 : angle 3.23348 ( 60) link_NAG-ASN : bond 0.00522 ( 51) link_NAG-ASN : angle 2.91919 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 0.608 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: H 103 TRP cc_start: 0.8812 (m100) cc_final: 0.8531 (m100) REVERT: L 37 GLN cc_start: 0.7600 (tp40) cc_final: 0.6863 (tp40) REVERT: L 42 GLN cc_start: 0.7958 (mt0) cc_final: 0.7584 (mt0) REVERT: L 82 ASP cc_start: 0.7553 (m-30) cc_final: 0.7255 (p0) REVERT: L 86 TYR cc_start: 0.7452 (m-80) cc_final: 0.7182 (m-10) REVERT: A 35 TRP cc_start: 0.7911 (m100) cc_final: 0.7599 (m-10) REVERT: A 78 ASP cc_start: 0.8016 (t0) cc_final: 0.7815 (t0) REVERT: A 106 GLU cc_start: 0.8438 (tt0) cc_final: 0.8148 (tp30) REVERT: A 120 VAL cc_start: 0.9203 (m) cc_final: 0.8932 (p) REVERT: A 486 TYR cc_start: 0.8679 (m-80) cc_final: 0.7915 (m-80) REVERT: B 535 MET cc_start: 0.8006 (mmm) cc_final: 0.7526 (mmm) REVERT: B 628 TRP cc_start: 0.9122 (m100) cc_final: 0.8321 (m100) REVERT: B 640 GLN cc_start: 0.8483 (mp10) cc_final: 0.8145 (mp10) REVERT: B 648 GLU cc_start: 0.7461 (tp30) cc_final: 0.6966 (tp30) REVERT: C 168 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7145 (mtmm) REVERT: C 210 PHE cc_start: 0.8174 (m-80) cc_final: 0.7562 (m-80) REVERT: C 217 TYR cc_start: 0.8657 (m-80) cc_final: 0.8088 (m-80) REVERT: C 278 THR cc_start: 0.8921 (p) cc_final: 0.8428 (t) REVERT: E 69 TRP cc_start: 0.8072 (m100) cc_final: 0.7702 (m100) REVERT: E 194 ILE cc_start: 0.8578 (tp) cc_final: 0.8167 (tt) REVERT: E 282 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8755 (mmmt) REVERT: E 426 MET cc_start: 0.7835 (tpt) cc_final: 0.7458 (tpt) REVERT: D 522 PHE cc_start: 0.9206 (t80) cc_final: 0.8932 (t80) REVERT: D 530 MET cc_start: 0.8409 (ttp) cc_final: 0.8150 (ttm) REVERT: D 538 THR cc_start: 0.9167 (p) cc_final: 0.8812 (p) REVERT: D 592 LEU cc_start: 0.8374 (tp) cc_final: 0.7720 (mp) REVERT: D 610 TRP cc_start: 0.8987 (t-100) cc_final: 0.8496 (t-100) REVERT: F 543 ASN cc_start: 0.8180 (m-40) cc_final: 0.7849 (t0) outliers start: 50 outliers final: 32 residues processed: 349 average time/residue: 0.1267 time to fit residues: 67.0230 Evaluate side-chains 286 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 116 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 64 optimal weight: 0.0770 chunk 28 optimal weight: 0.3980 overall best weight: 0.8458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 543 ASN B 625 ASN B 653 GLN E 258 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138469 restraints weight = 24332.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136567 restraints weight = 25370.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138594 restraints weight = 24530.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139562 restraints weight = 18838.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139801 restraints weight = 16837.037| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16435 Z= 0.163 Angle : 0.744 12.072 22482 Z= 0.360 Chirality : 0.048 0.267 2720 Planarity : 0.004 0.042 2735 Dihedral : 9.123 71.072 3654 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Rotamer: Outliers : 3.29 % Allowed : 12.27 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.62 (0.19), residues: 1867 helix: -0.05 (0.28), residues: 363 sheet: 0.12 (0.24), residues: 465 loop : -0.75 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 TYR 0.018 0.002 TYR H 79 PHE 0.026 0.002 PHE E 468 TRP 0.032 0.002 TRP B 610 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00378 (16323) covalent geometry : angle 0.69442 (22180) SS BOND : bond 0.00435 ( 34) SS BOND : angle 1.68549 ( 68) hydrogen bonds : bond 0.04952 ( 401) hydrogen bonds : angle 5.45371 ( 1029) link_ALPHA1-3 : bond 0.00923 ( 5) link_ALPHA1-3 : angle 2.46064 ( 15) link_ALPHA1-6 : bond 0.01141 ( 2) link_ALPHA1-6 : angle 2.16291 ( 6) link_BETA1-4 : bond 0.00629 ( 20) link_BETA1-4 : angle 2.77634 ( 60) link_NAG-ASN : bond 0.00430 ( 51) link_NAG-ASN : angle 2.53333 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.603 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: H 82 MET cc_start: 0.5012 (mmt) cc_final: 0.3657 (tpp) REVERT: H 103 TRP cc_start: 0.8936 (m100) cc_final: 0.8394 (m100) REVERT: L 37 GLN cc_start: 0.7082 (tp40) cc_final: 0.6575 (tp40) REVERT: L 86 TYR cc_start: 0.7419 (m-80) cc_final: 0.7127 (m-80) REVERT: A 106 GLU cc_start: 0.8510 (tt0) cc_final: 0.8241 (tp30) REVERT: A 168 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8093 (ttpt) REVERT: A 486 TYR cc_start: 0.8567 (m-80) cc_final: 0.7758 (m-80) REVERT: B 640 GLN cc_start: 0.8539 (mp10) cc_final: 0.8221 (mp10) REVERT: B 648 GLU cc_start: 0.7530 (tp30) cc_final: 0.7027 (tp30) REVERT: B 653 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6851 (pp30) REVERT: C 177 TYR cc_start: 0.8214 (m-80) cc_final: 0.7899 (m-80) REVERT: C 258 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: C 278 THR cc_start: 0.8935 (p) cc_final: 0.8454 (t) REVERT: E 69 TRP cc_start: 0.8069 (m100) cc_final: 0.7674 (m100) REVERT: E 194 ILE cc_start: 0.8429 (tp) cc_final: 0.8050 (tt) REVERT: E 258 GLN cc_start: 0.8093 (mt0) cc_final: 0.7856 (mt0) REVERT: E 349 LEU cc_start: 0.8890 (mt) cc_final: 0.8611 (mt) REVERT: E 426 MET cc_start: 0.7749 (tpt) cc_final: 0.7446 (tpt) REVERT: D 592 LEU cc_start: 0.8572 (tp) cc_final: 0.7770 (mt) REVERT: D 639 THR cc_start: 0.8646 (p) cc_final: 0.8109 (m) REVERT: F 546 SER cc_start: 0.6828 (p) cc_final: 0.6424 (m) REVERT: F 647 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7826 (tm-30) outliers start: 55 outliers final: 36 residues processed: 306 average time/residue: 0.1319 time to fit residues: 60.4770 Evaluate side-chains 259 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 74 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 168 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137515 restraints weight = 24295.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135863 restraints weight = 26523.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137916 restraints weight = 27018.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138841 restraints weight = 19726.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139024 restraints weight = 17625.172| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16435 Z= 0.138 Angle : 0.694 11.301 22482 Z= 0.336 Chirality : 0.047 0.282 2720 Planarity : 0.004 0.040 2735 Dihedral : 7.535 60.712 3653 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.79 % Rotamer: Outliers : 2.93 % Allowed : 13.76 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.19), residues: 1867 helix: 0.11 (0.28), residues: 363 sheet: 0.09 (0.23), residues: 502 loop : -0.76 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.020 0.002 TYR F 643 PHE 0.018 0.002 PHE E 93 TRP 0.021 0.002 TRP C 427 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00319 (16323) covalent geometry : angle 0.64671 (22180) SS BOND : bond 0.00483 ( 34) SS BOND : angle 1.61183 ( 68) hydrogen bonds : bond 0.04495 ( 401) hydrogen bonds : angle 5.23337 ( 1029) link_ALPHA1-3 : bond 0.00927 ( 5) link_ALPHA1-3 : angle 2.40091 ( 15) link_ALPHA1-6 : bond 0.00884 ( 2) link_ALPHA1-6 : angle 1.87358 ( 6) link_BETA1-4 : bond 0.00478 ( 20) link_BETA1-4 : angle 2.54963 ( 60) link_NAG-ASN : bond 0.00373 ( 51) link_NAG-ASN : angle 2.41319 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6915 (ptp-170) REVERT: H 82 MET cc_start: 0.4542 (mmt) cc_final: 0.3433 (tpt) REVERT: H 100 ASP cc_start: 0.7785 (t0) cc_final: 0.7518 (t0) REVERT: H 100 TYR cc_start: 0.8419 (m-10) cc_final: 0.7853 (m-10) REVERT: H 103 TRP cc_start: 0.9017 (m100) cc_final: 0.8514 (m100) REVERT: L 37 GLN cc_start: 0.6649 (tp40) cc_final: 0.6007 (tp40) REVERT: A 78 ASP cc_start: 0.7701 (t0) cc_final: 0.7370 (p0) REVERT: A 106 GLU cc_start: 0.8551 (tt0) cc_final: 0.8289 (tp30) REVERT: A 150 MET cc_start: 0.7257 (mmt) cc_final: 0.6545 (mmt) REVERT: A 168 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8126 (ttpt) REVERT: A 486 TYR cc_start: 0.8561 (m-80) cc_final: 0.7768 (m-80) REVERT: C 97 LYS cc_start: 0.7643 (tptp) cc_final: 0.7278 (tptp) REVERT: C 168 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7404 (mtpt) REVERT: C 177 TYR cc_start: 0.8164 (m-80) cc_final: 0.7833 (m-80) REVERT: E 69 TRP cc_start: 0.8074 (m100) cc_final: 0.7702 (m100) REVERT: E 194 ILE cc_start: 0.8410 (tp) cc_final: 0.8013 (tt) REVERT: E 426 MET cc_start: 0.7761 (tpt) cc_final: 0.7421 (tpt) REVERT: D 592 LEU cc_start: 0.8705 (tp) cc_final: 0.7903 (mt) REVERT: D 639 THR cc_start: 0.8624 (p) cc_final: 0.8055 (m) REVERT: F 546 SER cc_start: 0.6829 (p) cc_final: 0.6457 (m) REVERT: F 647 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7853 (tm-30) outliers start: 49 outliers final: 37 residues processed: 283 average time/residue: 0.1338 time to fit residues: 56.4684 Evaluate side-chains 257 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 127 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 134 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN C 170 GLN C 289 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126097 restraints weight = 24280.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124305 restraints weight = 26730.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126052 restraints weight = 26134.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126908 restraints weight = 20278.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127217 restraints weight = 18570.891| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16435 Z= 0.126 Angle : 0.656 10.551 22482 Z= 0.317 Chirality : 0.046 0.296 2720 Planarity : 0.004 0.049 2735 Dihedral : 6.590 59.044 3652 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 3.29 % Allowed : 14.60 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1867 helix: 0.32 (0.28), residues: 354 sheet: 0.02 (0.23), residues: 500 loop : -0.75 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.014 0.001 TYR L 86 PHE 0.032 0.002 PHE H 29 TRP 0.022 0.001 TRP H 47 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00293 (16323) covalent geometry : angle 0.60946 (22180) SS BOND : bond 0.00489 ( 34) SS BOND : angle 1.45226 ( 68) hydrogen bonds : bond 0.04084 ( 401) hydrogen bonds : angle 5.10964 ( 1029) link_ALPHA1-3 : bond 0.00938 ( 5) link_ALPHA1-3 : angle 2.30799 ( 15) link_ALPHA1-6 : bond 0.00660 ( 2) link_ALPHA1-6 : angle 1.32766 ( 6) link_BETA1-4 : bond 0.00446 ( 20) link_BETA1-4 : angle 2.26450 ( 60) link_NAG-ASN : bond 0.00326 ( 51) link_NAG-ASN : angle 2.40820 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.584 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: H 82 MET cc_start: 0.4905 (mmt) cc_final: 0.3621 (tpt) REVERT: H 103 TRP cc_start: 0.9036 (m100) cc_final: 0.8569 (m100) REVERT: L 86 TYR cc_start: 0.7936 (m-80) cc_final: 0.7241 (m-10) REVERT: L 87 TYR cc_start: 0.7380 (m-80) cc_final: 0.7117 (m-80) REVERT: A 78 ASP cc_start: 0.7824 (t0) cc_final: 0.7386 (p0) REVERT: A 150 MET cc_start: 0.7238 (mmt) cc_final: 0.6642 (mmt) REVERT: A 168 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8211 (ttpt) REVERT: A 426 MET cc_start: 0.7189 (ttp) cc_final: 0.5942 (tpt) REVERT: A 486 TYR cc_start: 0.8525 (m-80) cc_final: 0.7747 (m-80) REVERT: B 647 GLU cc_start: 0.7871 (tp30) cc_final: 0.7236 (tp30) REVERT: B 648 GLU cc_start: 0.7225 (tp30) cc_final: 0.6885 (tp30) REVERT: C 132 THR cc_start: 0.9195 (p) cc_final: 0.8953 (t) REVERT: C 168 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7399 (mtpt) REVERT: C 177 TYR cc_start: 0.8133 (m-80) cc_final: 0.7789 (m-80) REVERT: C 258 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: C 465 THR cc_start: 0.5742 (m) cc_final: 0.5378 (p) REVERT: E 150 MET cc_start: 0.6223 (mmt) cc_final: 0.5911 (mmt) REVERT: E 194 ILE cc_start: 0.8446 (tp) cc_final: 0.8073 (tt) REVERT: E 426 MET cc_start: 0.7702 (tpt) cc_final: 0.7385 (tpt) REVERT: D 592 LEU cc_start: 0.8754 (tp) cc_final: 0.8108 (mt) REVERT: F 546 SER cc_start: 0.6780 (p) cc_final: 0.6503 (m) REVERT: F 633 LYS cc_start: 0.8867 (tttm) cc_final: 0.8608 (mmmm) REVERT: F 647 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7751 (tm-30) outliers start: 55 outliers final: 36 residues processed: 274 average time/residue: 0.1303 time to fit residues: 53.5103 Evaluate side-chains 255 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN C 289 ASN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125525 restraints weight = 24238.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123950 restraints weight = 26591.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125739 restraints weight = 25743.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126775 restraints weight = 19803.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126999 restraints weight = 17917.990| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16435 Z= 0.122 Angle : 0.635 10.233 22482 Z= 0.311 Chirality : 0.046 0.299 2720 Planarity : 0.004 0.043 2735 Dihedral : 6.097 57.920 3648 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 3.23 % Allowed : 15.38 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.48 (0.19), residues: 1867 helix: 0.59 (0.29), residues: 351 sheet: 0.05 (0.23), residues: 500 loop : -0.81 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.013 0.001 TYR A 484 PHE 0.029 0.002 PHE H 29 TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00278 (16323) covalent geometry : angle 0.59099 (22180) SS BOND : bond 0.00419 ( 34) SS BOND : angle 1.76152 ( 68) hydrogen bonds : bond 0.03831 ( 401) hydrogen bonds : angle 4.96674 ( 1029) link_ALPHA1-3 : bond 0.00876 ( 5) link_ALPHA1-3 : angle 2.28991 ( 15) link_ALPHA1-6 : bond 0.00639 ( 2) link_ALPHA1-6 : angle 1.20256 ( 6) link_BETA1-4 : bond 0.00416 ( 20) link_BETA1-4 : angle 2.13478 ( 60) link_NAG-ASN : bond 0.00272 ( 51) link_NAG-ASN : angle 2.22256 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 0.593 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: H 82 MET cc_start: 0.4924 (mmt) cc_final: 0.3533 (tpt) REVERT: H 100 ASP cc_start: 0.7788 (t0) cc_final: 0.7489 (t0) REVERT: H 100 TYR cc_start: 0.8508 (m-10) cc_final: 0.8188 (m-10) REVERT: H 103 TRP cc_start: 0.9071 (m100) cc_final: 0.8541 (m100) REVERT: L 32 TYR cc_start: 0.8099 (m-80) cc_final: 0.7804 (m-80) REVERT: L 37 GLN cc_start: 0.6764 (tp-100) cc_final: 0.5663 (tp40) REVERT: L 82 ASP cc_start: 0.7966 (p0) cc_final: 0.7391 (t0) REVERT: L 85 VAL cc_start: 0.8611 (m) cc_final: 0.8361 (m) REVERT: L 86 TYR cc_start: 0.7811 (m-80) cc_final: 0.5832 (m-10) REVERT: A 78 ASP cc_start: 0.7805 (t0) cc_final: 0.7383 (p0) REVERT: A 150 MET cc_start: 0.7246 (mmt) cc_final: 0.6694 (mmt) REVERT: A 168 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8297 (ttpt) REVERT: A 426 MET cc_start: 0.7111 (ttp) cc_final: 0.5540 (tpt) REVERT: A 486 TYR cc_start: 0.8406 (m-80) cc_final: 0.7715 (m-80) REVERT: B 648 GLU cc_start: 0.7274 (tp30) cc_final: 0.6965 (tp30) REVERT: C 132 THR cc_start: 0.9137 (p) cc_final: 0.8898 (t) REVERT: C 177 TYR cc_start: 0.8146 (m-80) cc_final: 0.7807 (m-80) REVERT: C 258 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: C 465 THR cc_start: 0.5733 (m) cc_final: 0.5439 (p) REVERT: E 352 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: E 426 MET cc_start: 0.7746 (tpt) cc_final: 0.7420 (tpt) REVERT: D 530 MET cc_start: 0.8630 (ttp) cc_final: 0.8287 (ttp) REVERT: D 592 LEU cc_start: 0.8757 (tp) cc_final: 0.8124 (mt) REVERT: F 633 LYS cc_start: 0.8858 (tttm) cc_final: 0.8637 (mmmm) REVERT: F 647 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7709 (tm-30) outliers start: 54 outliers final: 37 residues processed: 276 average time/residue: 0.1300 time to fit residues: 53.9630 Evaluate side-chains 259 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 161 optimal weight: 0.0370 chunk 66 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 183 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 249 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125866 restraints weight = 24187.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124102 restraints weight = 26765.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125815 restraints weight = 25546.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126575 restraints weight = 20175.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126723 restraints weight = 18982.042| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.003 0.047 16435 Z= 0.118 Angle : 0.661 25.518 22482 Z= 0.314 Chirality : 0.046 0.332 2720 Planarity : 0.004 0.046 2735 Dihedral : 6.073 57.468 3648 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 3.05 % Allowed : 16.10 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.19), residues: 1867 helix: 0.67 (0.29), residues: 351 sheet: -0.08 (0.23), residues: 516 loop : -0.83 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.027 0.001 TYR A 484 PHE 0.025 0.002 PHE H 29 TRP 0.024 0.001 TRP H 47 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00273 (16323) covalent geometry : angle 0.59017 (22180) SS BOND : bond 0.00406 ( 34) SS BOND : angle 1.43260 ( 68) hydrogen bonds : bond 0.03749 ( 401) hydrogen bonds : angle 4.91184 ( 1029) link_ALPHA1-3 : bond 0.00825 ( 5) link_ALPHA1-3 : angle 2.21688 ( 15) link_ALPHA1-6 : bond 0.00772 ( 2) link_ALPHA1-6 : angle 1.25798 ( 6) link_BETA1-4 : bond 0.00414 ( 20) link_BETA1-4 : angle 2.06047 ( 60) link_NAG-ASN : bond 0.00274 ( 51) link_NAG-ASN : angle 3.26840 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.6507 (t60) cc_final: 0.5739 (t60) REVERT: H 82 MET cc_start: 0.4970 (mmt) cc_final: 0.3602 (tpt) REVERT: H 100 ASP cc_start: 0.7821 (t0) cc_final: 0.7360 (t0) REVERT: H 100 TYR cc_start: 0.8451 (m-10) cc_final: 0.8007 (m-10) REVERT: H 103 TRP cc_start: 0.9037 (m100) cc_final: 0.8563 (m100) REVERT: L 32 TYR cc_start: 0.8143 (m-80) cc_final: 0.7908 (m-80) REVERT: L 37 GLN cc_start: 0.6685 (tp-100) cc_final: 0.5687 (tp40) REVERT: L 62 PHE cc_start: 0.6759 (m-80) cc_final: 0.6164 (m-80) REVERT: L 82 ASP cc_start: 0.8012 (p0) cc_final: 0.7375 (t0) REVERT: L 85 VAL cc_start: 0.8606 (m) cc_final: 0.8350 (m) REVERT: L 86 TYR cc_start: 0.8000 (m-80) cc_final: 0.5675 (m-10) REVERT: A 78 ASP cc_start: 0.7830 (t0) cc_final: 0.7341 (p0) REVERT: A 150 MET cc_start: 0.7307 (mmt) cc_final: 0.6776 (mmt) REVERT: A 168 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8305 (ttpt) REVERT: A 426 MET cc_start: 0.7045 (ttp) cc_final: 0.5676 (tpt) REVERT: A 486 TYR cc_start: 0.8260 (m-80) cc_final: 0.7631 (m-80) REVERT: B 648 GLU cc_start: 0.7284 (tp30) cc_final: 0.6977 (tp30) REVERT: C 132 THR cc_start: 0.9105 (p) cc_final: 0.8881 (t) REVERT: C 140 ASP cc_start: 0.6140 (t0) cc_final: 0.5913 (t0) REVERT: C 177 TYR cc_start: 0.8195 (m-80) cc_final: 0.7872 (m-80) REVERT: C 258 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: C 465 THR cc_start: 0.5690 (m) cc_final: 0.5323 (p) REVERT: E 295 ASN cc_start: 0.6410 (m-40) cc_final: 0.6065 (m-40) REVERT: E 352 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7358 (t-90) REVERT: E 426 MET cc_start: 0.7729 (tpt) cc_final: 0.7445 (tpt) REVERT: D 530 MET cc_start: 0.8606 (ttp) cc_final: 0.8268 (ttp) REVERT: D 592 LEU cc_start: 0.8788 (tp) cc_final: 0.8135 (mt) REVERT: F 633 LYS cc_start: 0.8810 (tttm) cc_final: 0.8585 (mmmm) REVERT: F 647 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7667 (tm-30) outliers start: 51 outliers final: 40 residues processed: 266 average time/residue: 0.1251 time to fit residues: 50.4755 Evaluate side-chains 265 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 164 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN A 287 GLN B 653 GLN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.159569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126058 restraints weight = 24388.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126806 restraints weight = 29104.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128028 restraints weight = 23312.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128594 restraints weight = 17725.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128961 restraints weight = 16789.865| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16435 Z= 0.121 Angle : 0.644 21.700 22482 Z= 0.309 Chirality : 0.046 0.283 2720 Planarity : 0.003 0.042 2735 Dihedral : 5.879 56.719 3648 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.75 % Allowed : 16.70 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1867 helix: 0.76 (0.29), residues: 351 sheet: -0.08 (0.23), residues: 500 loop : -0.83 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.026 0.001 TYR A 484 PHE 0.015 0.001 PHE E 93 TRP 0.022 0.001 TRP H 47 HIS 0.008 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00281 (16323) covalent geometry : angle 0.58353 (22180) SS BOND : bond 0.00413 ( 34) SS BOND : angle 1.35419 ( 68) hydrogen bonds : bond 0.03699 ( 401) hydrogen bonds : angle 4.89175 ( 1029) link_ALPHA1-3 : bond 0.00791 ( 5) link_ALPHA1-3 : angle 2.16367 ( 15) link_ALPHA1-6 : bond 0.00747 ( 2) link_ALPHA1-6 : angle 1.26241 ( 6) link_BETA1-4 : bond 0.00406 ( 20) link_BETA1-4 : angle 2.01076 ( 60) link_NAG-ASN : bond 0.00385 ( 51) link_NAG-ASN : angle 2.94712 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6638 (ptp-170) REVERT: H 47 TRP cc_start: 0.6589 (t60) cc_final: 0.6343 (t60) REVERT: H 82 MET cc_start: 0.4554 (mmt) cc_final: 0.3521 (tpt) REVERT: H 100 ASP cc_start: 0.7798 (t0) cc_final: 0.7236 (t0) REVERT: H 100 TYR cc_start: 0.8491 (m-10) cc_final: 0.7906 (m-10) REVERT: H 103 TRP cc_start: 0.8852 (m100) cc_final: 0.8445 (m100) REVERT: L 37 GLN cc_start: 0.6629 (tp-100) cc_final: 0.5847 (tp40) REVERT: L 62 PHE cc_start: 0.6164 (m-80) cc_final: 0.5624 (m-80) REVERT: L 82 ASP cc_start: 0.7866 (p0) cc_final: 0.7259 (t0) REVERT: L 85 VAL cc_start: 0.8721 (m) cc_final: 0.8452 (p) REVERT: L 86 TYR cc_start: 0.7823 (m-80) cc_final: 0.5596 (m-10) REVERT: A 78 ASP cc_start: 0.7693 (t0) cc_final: 0.7438 (t0) REVERT: A 150 MET cc_start: 0.7358 (mmt) cc_final: 0.6844 (mmt) REVERT: A 168 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8290 (ttpt) REVERT: A 426 MET cc_start: 0.7052 (ttp) cc_final: 0.5681 (tpt) REVERT: A 486 TYR cc_start: 0.8290 (m-80) cc_final: 0.7613 (m-80) REVERT: B 648 GLU cc_start: 0.7283 (tp30) cc_final: 0.7007 (tp30) REVERT: C 132 THR cc_start: 0.9062 (p) cc_final: 0.8849 (t) REVERT: C 140 ASP cc_start: 0.5999 (t0) cc_final: 0.5763 (t0) REVERT: C 258 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: C 465 THR cc_start: 0.6304 (m) cc_final: 0.5833 (p) REVERT: E 295 ASN cc_start: 0.6346 (m-40) cc_final: 0.5956 (m-40) REVERT: E 352 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: E 426 MET cc_start: 0.7773 (tpt) cc_final: 0.7408 (tpt) REVERT: D 530 MET cc_start: 0.8556 (ttp) cc_final: 0.8264 (ttp) REVERT: D 592 LEU cc_start: 0.8714 (tp) cc_final: 0.8201 (mt) REVERT: F 633 LYS cc_start: 0.8807 (tttm) cc_final: 0.8592 (mmmm) REVERT: F 647 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 46 outliers final: 38 residues processed: 253 average time/residue: 0.1245 time to fit residues: 47.7798 Evaluate side-chains 258 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 352 HIS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 81 optimal weight: 0.0020 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124732 restraints weight = 24256.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125101 restraints weight = 25803.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126464 restraints weight = 23058.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127383 restraints weight = 17490.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127680 restraints weight = 16150.021| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16435 Z= 0.110 Angle : 0.629 20.301 22482 Z= 0.302 Chirality : 0.045 0.254 2720 Planarity : 0.004 0.049 2735 Dihedral : 5.719 56.593 3648 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 17.53 % Favored : 80.01 % 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: -0.49 (0.19), residues: 1867 helix: 0.86 (0.29), residues: 351 sheet: -0.11 (0.23), residues: 500 loop : -0.83 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.027 0.001 TYR A 484 PHE 0.027 0.001 PHE H 29 TRP 0.021 0.001 TRP H 47 HIS 0.010 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00254 (16323) covalent geometry : angle 0.57562 (22180) SS BOND : bond 0.00377 ( 34) SS BOND : angle 1.31417 ( 68) hydrogen bonds : bond 0.03533 ( 401) hydrogen bonds : angle 4.79675 ( 1029) link_ALPHA1-3 : bond 0.00764 ( 5) link_ALPHA1-3 : angle 2.05863 ( 15) link_ALPHA1-6 : bond 0.00775 ( 2) link_ALPHA1-6 : angle 1.25809 ( 6) link_BETA1-4 : bond 0.00425 ( 20) link_BETA1-4 : angle 1.94771 ( 60) link_NAG-ASN : bond 0.00375 ( 51) link_NAG-ASN : angle 2.70756 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.617 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: H 38 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.7226 (ptp-170) REVERT: H 82 MET cc_start: 0.4946 (mmt) cc_final: 0.3577 (tpt) REVERT: H 100 ASP cc_start: 0.7877 (t0) cc_final: 0.7514 (t0) REVERT: H 103 TRP cc_start: 0.9010 (m100) cc_final: 0.8539 (m100) REVERT: L 37 GLN cc_start: 0.6360 (tp-100) cc_final: 0.5301 (tp40) REVERT: L 62 PHE cc_start: 0.6429 (m-80) cc_final: 0.5741 (m-80) REVERT: L 82 ASP cc_start: 0.7892 (p0) cc_final: 0.7367 (t0) REVERT: L 85 VAL cc_start: 0.8588 (m) cc_final: 0.8252 (p) REVERT: L 86 TYR cc_start: 0.8085 (m-80) cc_final: 0.5898 (m-10) REVERT: A 78 ASP cc_start: 0.7839 (t0) cc_final: 0.7585 (t0) REVERT: A 150 MET cc_start: 0.7310 (mmt) cc_final: 0.6805 (mmt) REVERT: A 168 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8313 (ttpt) REVERT: A 426 MET cc_start: 0.7104 (ttp) cc_final: 0.5869 (tpt) REVERT: A 486 TYR cc_start: 0.8166 (m-80) cc_final: 0.7590 (m-80) REVERT: B 648 GLU cc_start: 0.7308 (tp30) cc_final: 0.7106 (tp30) REVERT: C 132 THR cc_start: 0.9023 (p) cc_final: 0.8799 (t) REVERT: C 140 ASP cc_start: 0.6220 (t0) cc_final: 0.5977 (t0) REVERT: C 168 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7328 (mtmm) REVERT: C 465 THR cc_start: 0.6385 (m) cc_final: 0.5943 (p) REVERT: E 295 ASN cc_start: 0.6224 (m-40) cc_final: 0.5865 (m-40) REVERT: E 426 MET cc_start: 0.7722 (tpt) cc_final: 0.7429 (tpt) REVERT: D 530 MET cc_start: 0.8586 (ttp) cc_final: 0.8384 (ttm) REVERT: D 592 LEU cc_start: 0.8664 (tp) cc_final: 0.8150 (mt) REVERT: D 625 ASN cc_start: 0.8073 (t0) cc_final: 0.7781 (t0) REVERT: D 639 THR cc_start: 0.8476 (p) cc_final: 0.7996 (m) REVERT: F 633 LYS cc_start: 0.8824 (tttm) cc_final: 0.8613 (mmmm) REVERT: F 647 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7462 (tm-30) outliers start: 41 outliers final: 37 residues processed: 255 average time/residue: 0.1288 time to fit residues: 49.7417 Evaluate side-chains 259 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122274 restraints weight = 24532.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121848 restraints weight = 27851.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123458 restraints weight = 24740.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124673 restraints weight = 18550.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125002 restraints weight = 16511.033| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16435 Z= 0.138 Angle : 0.647 19.726 22482 Z= 0.313 Chirality : 0.046 0.249 2720 Planarity : 0.004 0.062 2735 Dihedral : 5.761 55.408 3648 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.51 % Allowed : 18.01 % Favored : 79.47 % 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: -0.48 (0.20), residues: 1867 helix: 0.89 (0.29), residues: 351 sheet: -0.16 (0.23), residues: 496 loop : -0.80 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.028 0.002 TYR A 484 PHE 0.019 0.002 PHE E 53 TRP 0.031 0.001 TRP H 47 HIS 0.010 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00326 (16323) covalent geometry : angle 0.59689 (22180) SS BOND : bond 0.00417 ( 34) SS BOND : angle 1.42116 ( 68) hydrogen bonds : bond 0.03786 ( 401) hydrogen bonds : angle 4.82683 ( 1029) link_ALPHA1-3 : bond 0.00715 ( 5) link_ALPHA1-3 : angle 2.05362 ( 15) link_ALPHA1-6 : bond 0.00728 ( 2) link_ALPHA1-6 : angle 1.29554 ( 6) link_BETA1-4 : bond 0.00396 ( 20) link_BETA1-4 : angle 1.97456 ( 60) link_NAG-ASN : bond 0.00365 ( 51) link_NAG-ASN : angle 2.64118 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.695 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: H 82 MET cc_start: 0.4962 (mmt) cc_final: 0.3764 (tpt) REVERT: H 100 ASP cc_start: 0.7998 (t0) cc_final: 0.7657 (t0) REVERT: H 103 TRP cc_start: 0.9031 (m100) cc_final: 0.8512 (m100) REVERT: L 37 GLN cc_start: 0.6301 (tp-100) cc_final: 0.5700 (tp40) REVERT: L 62 PHE cc_start: 0.6420 (m-80) cc_final: 0.6085 (m-80) REVERT: L 82 ASP cc_start: 0.7825 (p0) cc_final: 0.7156 (t0) REVERT: A 78 ASP cc_start: 0.7906 (t0) cc_final: 0.7634 (t0) REVERT: A 168 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8359 (ttpt) REVERT: A 426 MET cc_start: 0.7194 (ttp) cc_final: 0.5777 (tpt) REVERT: A 486 TYR cc_start: 0.8479 (m-80) cc_final: 0.7693 (m-80) REVERT: C 112 TRP cc_start: 0.8302 (t-100) cc_final: 0.8069 (t-100) REVERT: C 132 THR cc_start: 0.9043 (p) cc_final: 0.8802 (t) REVERT: C 140 ASP cc_start: 0.6079 (t0) cc_final: 0.5845 (t0) REVERT: C 168 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7461 (mtmm) REVERT: E 295 ASN cc_start: 0.6486 (m-40) cc_final: 0.6005 (m-40) REVERT: E 349 LEU cc_start: 0.8563 (tp) cc_final: 0.8356 (mp) REVERT: E 426 MET cc_start: 0.7871 (tpt) cc_final: 0.7572 (tpt) REVERT: D 530 MET cc_start: 0.8541 (ttp) cc_final: 0.8335 (ttm) REVERT: D 625 ASN cc_start: 0.8045 (t0) cc_final: 0.7818 (t0) REVERT: D 639 THR cc_start: 0.8470 (p) cc_final: 0.8002 (m) REVERT: F 647 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7665 (tm-30) outliers start: 42 outliers final: 39 residues processed: 254 average time/residue: 0.1374 time to fit residues: 52.2613 Evaluate side-chains 255 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 13 optimal weight: 30.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100HHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN C 315 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121999 restraints weight = 24264.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121691 restraints weight = 27763.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123731 restraints weight = 23856.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125026 restraints weight = 17832.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125593 restraints weight = 16624.182| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16435 Z= 0.124 Angle : 0.630 19.070 22482 Z= 0.306 Chirality : 0.045 0.237 2720 Planarity : 0.004 0.041 2735 Dihedral : 5.710 55.825 3648 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 2.81 % Allowed : 17.89 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1867 helix: 0.98 (0.29), residues: 351 sheet: -0.16 (0.24), residues: 491 loop : -0.87 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.026 0.002 TYR A 484 PHE 0.017 0.001 PHE H 29 TRP 0.045 0.001 TRP H 47 HIS 0.010 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00290 (16323) covalent geometry : angle 0.58199 (22180) SS BOND : bond 0.00390 ( 34) SS BOND : angle 1.27624 ( 68) hydrogen bonds : bond 0.03621 ( 401) hydrogen bonds : angle 4.83417 ( 1029) link_ALPHA1-3 : bond 0.00716 ( 5) link_ALPHA1-3 : angle 1.96710 ( 15) link_ALPHA1-6 : bond 0.00792 ( 2) link_ALPHA1-6 : angle 1.27415 ( 6) link_BETA1-4 : bond 0.00406 ( 20) link_BETA1-4 : angle 1.90885 ( 60) link_NAG-ASN : bond 0.00374 ( 51) link_NAG-ASN : angle 2.55830 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.29 seconds wall clock time: 42 minutes 54.02 seconds (2574.02 seconds total)