Starting phenix.real_space_refine on Sun Aug 24 17:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8b_44341/08_2025/9b8b_44341.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 128 5.16 5 C 13138 2.51 5 N 3531 2.21 5 O 4210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21007 Number of models: 1 Model: "" Number of chains: 31 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1014 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} 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: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3322 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Chain: "B" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 957 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3377 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 957 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3299 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 936 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 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: 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: "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: 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: "S" 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: "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: 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: "W" 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 5.44, per 1000 atoms: 0.26 Number of scatterers: 21007 At special positions: 0 Unit cell: (119.016, 124.236, 184.788, 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 128 16.00 O 4210 8.00 N 3531 7.00 C 13138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 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 E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 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 BETA1-4 " 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 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 241 " " NAG A 612 " - " ASN A 301 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 156 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 276 " " NAG C 609 " - " ASN C 289 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 301 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 355 " " NAG C 614 " - " ASN C 392 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 197 " " NAG D 603 " - " ASN D 234 " " NAG D 604 " - " ASN D 241 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 289 " " NAG D 607 " - " ASN D 295 " " NAG D 608 " - " ASN D 332 " " NAG D 609 " - " ASN D 301 " " NAG D 610 " - " ASN D 339 " " NAG D 611 " - " ASN D 392 " " NAG D 612 " - " ASN D 448 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG E 704 " - " ASN E 625 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 625 " " NAG F 704 " - " ASN F 637 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN D 156 " " NAG W 1 " - " ASN D 160 " " NAG X 1 " - " ASN D 262 " " NAG Y 1 " - " ASN D 386 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 879.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4690 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 42 sheets defined 19.3% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.653A pdb=" N VAL L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.994A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.500A pdb=" N LYS K 64 " --> pdb=" O ASP K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.531A pdb=" N THR M 87 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.415A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.220A 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 removed outlier: 4.035A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.411A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.411A 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 543 removed outlier: 3.977A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.270A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.700A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 573 through 596 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.654A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 476 through 484 removed outlier: 4.842A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.535A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 635 through 661 removed outlier: 4.580A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.483A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.660A pdb=" N GLU L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AA6, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.644A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE G 97 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.461A pdb=" N LEU I 11 " --> pdb=" O SER I 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.632A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET I 34 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100G through 103 Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AB7, first strand: chain 'N' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 11 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.175A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.662A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.657A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 260 current: chain 'A' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 287 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 465 through 470 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 294 through 311 removed outlier: 6.463A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 303 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 309 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN A 314 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 314 through 323 current: chain 'A' and resid 381 through 385 removed outlier: 3.938A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.303A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.546A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.799A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AD5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.193A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD7, 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 284 through 311 removed outlier: 6.505A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 303 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 314 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 314 through 323 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 465 through 470 Processing sheet with id=AD8, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.198A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE2, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE3, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AE4, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.997A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.652A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR D 303 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN D 314 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 314 through 323 current: chain 'D' and resid 381 through 385 removed outlier: 4.027A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 421 current: chain 'D' and resid 465 through 470 612 hydrogen bonds defined for protein. 1623 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: 4.10 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6583 1.34 - 1.46: 5341 1.46 - 1.58: 9313 1.58 - 1.71: 2 1.71 - 1.83: 175 Bond restraints: 21414 Sorted by residual: bond pdb=" N TYS H 100F" pdb=" CA TYS H 100F" ideal model delta sigma weight residual 1.458 1.525 -0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" N ARG C 166 " pdb=" CA ARG C 166 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.25e-02 6.40e+03 3.71e+00 bond pdb=" O3 TYS H 100D" pdb=" S TYS H 100D" ideal model delta sigma weight residual 1.458 1.420 0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" O3 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.458 1.422 0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" N VAL H 1 " pdb=" CA VAL H 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 ... (remaining 21409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 26702 1.48 - 2.96: 2019 2.96 - 4.45: 243 4.45 - 5.93: 73 5.93 - 7.41: 7 Bond angle restraints: 29044 Sorted by residual: angle pdb=" N TRP F 596 " pdb=" CA TRP F 596 " pdb=" C TRP F 596 " ideal model delta sigma weight residual 110.35 105.43 4.92 1.38e+00 5.25e-01 1.27e+01 angle pdb=" N ALA K 100 " pdb=" CA ALA K 100 " pdb=" C ALA K 100 " ideal model delta sigma weight residual 110.80 118.21 -7.41 2.13e+00 2.20e-01 1.21e+01 angle pdb=" C GLY A 379 " pdb=" N GLY A 380 " pdb=" CA GLY A 380 " ideal model delta sigma weight residual 121.41 127.84 -6.43 1.96e+00 2.60e-01 1.08e+01 angle pdb=" N ALA M 100 " pdb=" CA ALA M 100 " pdb=" C ALA M 100 " ideal model delta sigma weight residual 110.80 117.52 -6.72 2.13e+00 2.20e-01 9.94e+00 angle pdb=" N ASP G 85 " pdb=" CA ASP G 85 " pdb=" C ASP G 85 " ideal model delta sigma weight residual 110.80 117.47 -6.67 2.13e+00 2.20e-01 9.80e+00 ... (remaining 29039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 13154 21.17 - 42.34: 389 42.34 - 63.52: 122 63.52 - 84.69: 27 84.69 - 105.86: 17 Dihedral angle restraints: 13709 sinusoidal: 6378 harmonic: 7331 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.96 -65.96 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.90 39.90 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -124.16 38.16 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 13706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3196 0.106 - 0.212: 244 0.212 - 0.318: 4 0.318 - 0.424: 1 0.424 - 0.530: 1 Chirality restraints: 3446 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.03e+00 chirality pdb=" C1 NAG A 608 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG A 608 " pdb=" O5 NAG A 608 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN D 160 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3443 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 651 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN F 651 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN F 651 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN F 652 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 654 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU F 654 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU F 654 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS F 655 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 652 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C GLN F 652 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN F 652 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN F 653 " -0.018 2.00e-02 2.50e+03 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 107 2.53 - 3.12: 15151 3.12 - 3.71: 30743 3.71 - 4.31: 46312 4.31 - 4.90: 76945 Nonbonded interactions: 169258 Sorted by model distance: nonbonded pdb=" OE2 GLU H 100A" pdb=" NH2 ARG C 169 " model vdw 1.937 3.120 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.277 3.040 nonbonded pdb=" OG SER K 98 " pdb=" NH2 ARG A 500 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG A 350 " pdb=" O THR A 357 " model vdw 2.290 3.120 nonbonded pdb=" O PHE K 29 " pdb=" NH2 ARG K 71 " model vdw 2.291 3.120 ... (remaining 169253 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 56 or resid 82 through 295 or (resid 296 and (n \ ame N or name CA or name C or name O or name CB )) or resid 297 through 330 or ( \ resid 331 and (name N or name CA or name C or name O or name CB )) or resid 332 \ through 444 or (resid 445 and (name N or name CA or name C or name O or name CB \ )) or resid 446 through 457 or resid 463 through 612)) selection = (chain 'C' and (resid 32 through 56 or resid 82 through 330 or (resid 331 and (n \ ame N or name CA or name C or name O or name CB )) or resid 332 through 444 or ( \ resid 445 and (name N or name CA or name C or name O or name CB )) or resid 446 \ through 457 or resid 463 through 612)) selection = (chain 'D' and (resid 32 through 295 or (resid 296 and (name N or name CA or nam \ e C or name O or name CB )) or resid 297 through 612)) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 575 through 703)) selection = (chain 'E' and (resid 519 through 546 or resid 575 through 703)) selection = (chain 'F' and resid 519 through 703) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'I' selection = (chain 'K' and resid 2 through 112) selection = (chain 'M' and resid 2 through 112) } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'X' } 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 individual isotropic 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: 4.530 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: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.290 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.005 0.067 21523 Z= 0.236 Angle : 0.878 8.742 29336 Z= 0.466 Chirality : 0.055 0.530 3446 Planarity : 0.005 0.089 3622 Dihedral : 11.859 105.859 8914 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.05 % Allowed : 0.72 % Favored : 99.23 % 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 aren not related in a simple way. whole: 0.55 (0.16), residues: 2511 helix: 0.88 (0.26), residues: 371 sheet: 0.77 (0.18), residues: 697 loop : 0.11 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 166 TYR 0.025 0.003 TYR D 484 PHE 0.035 0.003 PHE D 176 TRP 0.029 0.002 TRP F 596 HIS 0.008 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00549 (21414) covalent geometry : angle 0.85402 (29044) SS BOND : bond 0.00513 ( 35) SS BOND : angle 1.64845 ( 70) hydrogen bonds : bond 0.13340 ( 612) hydrogen bonds : angle 6.90771 ( 1623) link_BETA1-4 : bond 0.00405 ( 14) link_BETA1-4 : angle 3.17667 ( 42) link_NAG-ASN : bond 0.00333 ( 60) link_NAG-ASN : angle 2.12906 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.7781 (t60) cc_final: 0.7470 (t60) REVERT: H 91 TYR cc_start: 0.7311 (p90) cc_final: 0.7107 (p90) REVERT: L 50 GLU cc_start: 0.6223 (mt-10) cc_final: 0.3330 (mt-10) REVERT: L 91 MET cc_start: 0.7915 (ttp) cc_final: 0.7572 (ttp) REVERT: G 14 SER cc_start: 0.8932 (m) cc_final: 0.8696 (p) REVERT: G 31 ASN cc_start: 0.8536 (m-40) cc_final: 0.8245 (m-40) REVERT: G 52 THR cc_start: 0.7469 (p) cc_final: 0.7248 (m) REVERT: G 56 SER cc_start: 0.8194 (m) cc_final: 0.7787 (p) REVERT: G 103 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7709 (mtp180) REVERT: I 3 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7337 (mm110) REVERT: I 72 ASP cc_start: 0.7295 (t0) cc_final: 0.6791 (t0) REVERT: I 74 SER cc_start: 0.8750 (m) cc_final: 0.8353 (p) REVERT: I 82 MET cc_start: 0.7942 (mtm) cc_final: 0.7537 (mtm) REVERT: J 91 TYR cc_start: 0.8477 (t80) cc_final: 0.8010 (t80) REVERT: K 81 GLN cc_start: 0.8181 (tp40) cc_final: 0.7951 (tp40) REVERT: K 105 GLN cc_start: 0.6340 (mm-40) cc_final: 0.6123 (pt0) REVERT: M 3 GLN cc_start: 0.8114 (mt0) cc_final: 0.7677 (mp10) REVERT: M 46 GLU cc_start: 0.7530 (tt0) cc_final: 0.7072 (tt0) REVERT: M 79 SER cc_start: 0.6732 (t) cc_final: 0.6419 (m) REVERT: M 82 SER cc_start: 0.8771 (m) cc_final: 0.8154 (p) REVERT: M 94 THR cc_start: 0.6764 (m) cc_final: 0.6013 (m) REVERT: N 14 SER cc_start: 0.8688 (m) cc_final: 0.8364 (p) REVERT: N 31 ASN cc_start: 0.8300 (m-40) cc_final: 0.7982 (m-40) REVERT: N 42 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8174 (mmmt) REVERT: N 52 THR cc_start: 0.7822 (p) cc_final: 0.7409 (p) REVERT: N 53 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7096 (mp10) REVERT: N 60 ASP cc_start: 0.8591 (p0) cc_final: 0.8345 (p0) REVERT: N 69 ASN cc_start: 0.7797 (m-40) cc_final: 0.7402 (m-40) REVERT: N 83 GLU cc_start: 0.7157 (tt0) cc_final: 0.6949 (tt0) REVERT: N 104 LEU cc_start: 0.7873 (tp) cc_final: 0.7534 (tp) REVERT: A 95 MET cc_start: 0.8685 (ptm) cc_final: 0.8361 (ptm) REVERT: A 232 LYS cc_start: 0.8447 (mttt) cc_final: 0.8196 (mtmm) REVERT: B 577 GLN cc_start: 0.8006 (tp40) cc_final: 0.7803 (tm-30) REVERT: D 169 ARG cc_start: 0.7515 (mmt90) cc_final: 0.7281 (mtm-85) REVERT: D 187 LEU cc_start: 0.8249 (tp) cc_final: 0.7963 (tp) REVERT: D 232 LYS cc_start: 0.7863 (mttt) cc_final: 0.7604 (mtmm) REVERT: D 314 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6999 (mt0) REVERT: D 477 ASP cc_start: 0.8048 (m-30) cc_final: 0.7764 (m-30) REVERT: F 626 MET cc_start: 0.8618 (ttm) cc_final: 0.8398 (ttm) REVERT: F 632 ASP cc_start: 0.8431 (t70) cc_final: 0.8223 (t0) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.1627 time to fit residues: 152.5589 Evaluate side-chains 344 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82AASN L 42 GLN G 38 GLN I 39 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN J 69 ASN K 39 GLN K 76 ASN M 39 GLN N 6 GLN N 38 GLN B 577 GLN B 591 GLN B 653 GLN E 543 ASN E 585 HIS D 363 GLN F 577 GLN F 590 GLN F 616 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119360 restraints weight = 30830.674| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.82 r_work: 0.3409 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21523 Z= 0.140 Angle : 0.637 22.342 29336 Z= 0.314 Chirality : 0.046 0.315 3446 Planarity : 0.004 0.048 3622 Dihedral : 8.172 59.903 4316 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.81 % Allowed : 8.74 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 2511 helix: 1.47 (0.27), residues: 382 sheet: 0.59 (0.18), residues: 741 loop : -0.08 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 617 TYR 0.019 0.001 TYR H 90 PHE 0.013 0.002 PHE A 53 TRP 0.020 0.001 TRP L 35 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00313 (21414) covalent geometry : angle 0.58609 (29044) SS BOND : bond 0.00374 ( 35) SS BOND : angle 1.11594 ( 70) hydrogen bonds : bond 0.04128 ( 612) hydrogen bonds : angle 5.28059 ( 1623) link_BETA1-4 : bond 0.00417 ( 14) link_BETA1-4 : angle 2.36416 ( 42) link_NAG-ASN : bond 0.00427 ( 60) link_NAG-ASN : angle 2.98321 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.7905 (ttp) cc_final: 0.7696 (ttp) REVERT: G 61 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8009 (ptt-90) REVERT: J 91 TYR cc_start: 0.8681 (t80) cc_final: 0.8235 (t80) REVERT: M 34 MET cc_start: 0.8604 (mmm) cc_final: 0.8400 (mmm) REVERT: M 46 GLU cc_start: 0.8576 (tt0) cc_final: 0.8337 (tt0) REVERT: M 79 SER cc_start: 0.7870 (t) cc_final: 0.7648 (m) REVERT: M 105 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7988 (pt0) REVERT: N 14 SER cc_start: 0.8822 (m) cc_final: 0.8594 (p) REVERT: N 104 LEU cc_start: 0.8434 (tp) cc_final: 0.8193 (tt) REVERT: A 130 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7794 (tp40) REVERT: A 232 LYS cc_start: 0.8566 (mttt) cc_final: 0.8247 (mtmm) REVERT: A 381 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7067 (mt-10) REVERT: A 477 ASP cc_start: 0.8746 (m-30) cc_final: 0.8499 (m-30) REVERT: B 657 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8458 (mt-10) REVERT: C 230 ASP cc_start: 0.7562 (t0) cc_final: 0.7215 (t0) REVERT: D 95 MET cc_start: 0.8345 (ptm) cc_final: 0.8136 (ptm) REVERT: D 104 MET cc_start: 0.8156 (ttt) cc_final: 0.7878 (ttt) REVERT: D 169 ARG cc_start: 0.7305 (mmt90) cc_final: 0.7012 (mtm-85) REVERT: D 232 LYS cc_start: 0.7664 (mttt) cc_final: 0.7401 (mtmm) REVERT: D 314 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6952 (mt0) REVERT: D 335 LYS cc_start: 0.6385 (mttt) cc_final: 0.5869 (pttm) REVERT: F 632 ASP cc_start: 0.8577 (t70) cc_final: 0.8373 (t0) outliers start: 40 outliers final: 23 residues processed: 397 average time/residue: 0.1374 time to fit residues: 86.0861 Evaluate side-chains 329 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 29 optimal weight: 0.0870 chunk 225 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN I 39 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN M 3 GLN D 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.150298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117232 restraints weight = 30971.545| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.83 r_work: 0.3385 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21523 Z= 0.121 Angle : 0.579 19.737 29336 Z= 0.285 Chirality : 0.045 0.358 3446 Planarity : 0.004 0.047 3622 Dihedral : 6.461 56.980 4316 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.91 % 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 aren not related in a simple way. whole: 0.50 (0.16), residues: 2511 helix: 1.85 (0.28), residues: 372 sheet: 0.58 (0.18), residues: 743 loop : -0.16 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 469 TYR 0.012 0.001 TYR H 90 PHE 0.015 0.001 PHE L 73 TRP 0.019 0.001 TRP A 112 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00270 (21414) covalent geometry : angle 0.53439 (29044) SS BOND : bond 0.00280 ( 35) SS BOND : angle 1.05319 ( 70) hydrogen bonds : bond 0.03733 ( 612) hydrogen bonds : angle 4.84935 ( 1623) link_BETA1-4 : bond 0.00417 ( 14) link_BETA1-4 : angle 2.12106 ( 42) link_NAG-ASN : bond 0.00542 ( 60) link_NAG-ASN : angle 2.67565 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.7910 (t60) cc_final: 0.7691 (t60) REVERT: G 53 GLN cc_start: 0.8838 (mp10) cc_final: 0.8551 (mp10) REVERT: M 34 MET cc_start: 0.8789 (mmm) cc_final: 0.8536 (mmt) REVERT: M 46 GLU cc_start: 0.8767 (tt0) cc_final: 0.8554 (tt0) REVERT: M 79 SER cc_start: 0.8136 (t) cc_final: 0.7846 (m) REVERT: M 81 GLN cc_start: 0.8250 (tp40) cc_final: 0.7985 (tp40) REVERT: M 105 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8093 (pt0) REVERT: N 69 ASN cc_start: 0.8532 (m-40) cc_final: 0.8295 (t0) REVERT: A 106 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: A 130 GLN cc_start: 0.8512 (mm-40) cc_final: 0.7825 (mt0) REVERT: A 381 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7687 (mt-10) REVERT: C 46 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8291 (mmtm) REVERT: C 230 ASP cc_start: 0.7797 (t0) cc_final: 0.7392 (t0) REVERT: C 434 MET cc_start: 0.8954 (ttp) cc_final: 0.8687 (ttp) REVERT: D 104 MET cc_start: 0.8306 (ttt) cc_final: 0.8059 (ttt) REVERT: D 169 ARG cc_start: 0.7536 (mmt90) cc_final: 0.7134 (mtm-85) REVERT: D 232 LYS cc_start: 0.7886 (mttt) cc_final: 0.7625 (mtmm) REVERT: D 314 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7020 (mt0) REVERT: D 325 ASP cc_start: 0.7436 (t0) cc_final: 0.7021 (t0) REVERT: D 335 LYS cc_start: 0.6557 (mttt) cc_final: 0.5909 (pttm) REVERT: F 632 ASP cc_start: 0.8789 (t70) cc_final: 0.8484 (t0) outliers start: 46 outliers final: 29 residues processed: 357 average time/residue: 0.1404 time to fit residues: 79.0840 Evaluate side-chains 323 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 620 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 34 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 178 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN A 33 ASN B 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114720 restraints weight = 31109.273| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.90 r_work: 0.3354 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21523 Z= 0.129 Angle : 0.560 19.593 29336 Z= 0.277 Chirality : 0.045 0.365 3446 Planarity : 0.003 0.048 3622 Dihedral : 5.705 58.193 4316 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.13 % Allowed : 11.18 % Favored : 86.69 % 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 aren not related in a simple way. whole: 0.49 (0.17), residues: 2511 helix: 1.90 (0.28), residues: 372 sheet: 0.61 (0.19), residues: 739 loop : -0.22 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.016 0.001 TYR M 27 PHE 0.014 0.001 PHE L 73 TRP 0.016 0.001 TRP A 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (21414) covalent geometry : angle 0.51525 (29044) SS BOND : bond 0.00288 ( 35) SS BOND : angle 0.99614 ( 70) hydrogen bonds : bond 0.03554 ( 612) hydrogen bonds : angle 4.66097 ( 1623) link_BETA1-4 : bond 0.00318 ( 14) link_BETA1-4 : angle 1.95619 ( 42) link_NAG-ASN : bond 0.00498 ( 60) link_NAG-ASN : angle 2.65208 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: L 91 MET cc_start: 0.7969 (ttp) cc_final: 0.7684 (ttp) REVERT: G 53 GLN cc_start: 0.8711 (mp10) cc_final: 0.8014 (mp10) REVERT: G 56 SER cc_start: 0.8338 (m) cc_final: 0.7965 (p) REVERT: M 46 GLU cc_start: 0.8558 (tt0) cc_final: 0.8339 (tt0) REVERT: M 79 SER cc_start: 0.8237 (t) cc_final: 0.7885 (m) REVERT: M 105 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8072 (pt0) REVERT: A 106 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 130 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7844 (mt0) REVERT: A 381 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7558 (mt-10) REVERT: C 46 LYS cc_start: 0.8352 (mmtp) cc_final: 0.8122 (mmtm) REVERT: C 230 ASP cc_start: 0.7577 (t0) cc_final: 0.7289 (t0) REVERT: D 95 MET cc_start: 0.8483 (ptm) cc_final: 0.8237 (ptm) REVERT: D 169 ARG cc_start: 0.7392 (mmt90) cc_final: 0.7072 (mtm-85) REVERT: D 232 LYS cc_start: 0.7814 (mttt) cc_final: 0.7585 (mtmm) REVERT: D 314 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7066 (mt0) REVERT: D 325 ASP cc_start: 0.7390 (t0) cc_final: 0.7039 (t0) REVERT: D 335 LYS cc_start: 0.6595 (mttt) cc_final: 0.5996 (pttm) REVERT: D 395 TRP cc_start: 0.7434 (m100) cc_final: 0.6988 (m100) outliers start: 47 outliers final: 33 residues processed: 350 average time/residue: 0.1393 time to fit residues: 76.7173 Evaluate side-chains 319 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 121 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 81 GLN K 39 GLN A 85 HIS C 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114029 restraints weight = 30980.267| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.93 r_work: 0.3326 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21523 Z= 0.125 Angle : 0.552 19.960 29336 Z= 0.270 Chirality : 0.045 0.504 3446 Planarity : 0.003 0.048 3622 Dihedral : 5.484 58.726 4316 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 12.27 % Favored : 85.97 % 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 aren not related in a simple way. whole: 0.42 (0.17), residues: 2511 helix: 1.77 (0.28), residues: 384 sheet: 0.57 (0.19), residues: 747 loop : -0.27 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 542 TYR 0.014 0.001 TYR M 27 PHE 0.012 0.001 PHE L 73 TRP 0.015 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00288 (21414) covalent geometry : angle 0.50695 (29044) SS BOND : bond 0.00323 ( 35) SS BOND : angle 0.88982 ( 70) hydrogen bonds : bond 0.03499 ( 612) hydrogen bonds : angle 4.53856 ( 1623) link_BETA1-4 : bond 0.00438 ( 14) link_BETA1-4 : angle 1.89683 ( 42) link_NAG-ASN : bond 0.00452 ( 60) link_NAG-ASN : angle 2.65182 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: L 91 MET cc_start: 0.7952 (ttp) cc_final: 0.7595 (ttp) REVERT: G 45 LYS cc_start: 0.8929 (pttt) cc_final: 0.8667 (ptmm) REVERT: G 56 SER cc_start: 0.8419 (m) cc_final: 0.8008 (p) REVERT: M 46 GLU cc_start: 0.8900 (tt0) cc_final: 0.8661 (tt0) REVERT: M 79 SER cc_start: 0.8401 (t) cc_final: 0.8089 (m) REVERT: M 105 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8137 (pt0) REVERT: A 106 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: A 130 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8055 (tp40) REVERT: A 188 TRP cc_start: 0.7914 (m100) cc_final: 0.7382 (m100) REVERT: A 381 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7884 (mt-10) REVERT: C 230 ASP cc_start: 0.7832 (t0) cc_final: 0.7464 (t0) REVERT: C 434 MET cc_start: 0.8884 (ttp) cc_final: 0.8589 (ttp) REVERT: E 616 ASN cc_start: 0.8851 (t0) cc_final: 0.8550 (p0) REVERT: D 169 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7156 (mtm-85) REVERT: D 230 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: D 232 LYS cc_start: 0.8007 (mttt) cc_final: 0.7720 (mtmm) REVERT: D 314 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7079 (mt0) REVERT: D 325 ASP cc_start: 0.7563 (t0) cc_final: 0.7143 (t0) REVERT: D 335 LYS cc_start: 0.6580 (mttt) cc_final: 0.6006 (pttm) REVERT: D 395 TRP cc_start: 0.7609 (m100) cc_final: 0.7142 (m100) outliers start: 39 outliers final: 30 residues processed: 325 average time/residue: 0.1424 time to fit residues: 72.4976 Evaluate side-chains 317 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 43 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN M 3 GLN B 540 GLN C 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112395 restraints weight = 30898.779| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.90 r_work: 0.3292 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21523 Z= 0.127 Angle : 0.562 19.611 29336 Z= 0.276 Chirality : 0.046 0.496 3446 Planarity : 0.003 0.046 3622 Dihedral : 5.393 58.876 4316 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 2.40 % Allowed : 12.40 % Favored : 85.20 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2511 helix: 1.77 (0.28), residues: 386 sheet: 0.57 (0.19), residues: 724 loop : -0.28 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.015 0.001 TYR K 27 PHE 0.012 0.001 PHE L 73 TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (21414) covalent geometry : angle 0.51351 (29044) SS BOND : bond 0.00236 ( 35) SS BOND : angle 0.89168 ( 70) hydrogen bonds : bond 0.03445 ( 612) hydrogen bonds : angle 4.49828 ( 1623) link_BETA1-4 : bond 0.00389 ( 14) link_BETA1-4 : angle 1.82700 ( 42) link_NAG-ASN : bond 0.00516 ( 60) link_NAG-ASN : angle 2.80044 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.7844 (ttp) cc_final: 0.7428 (ttp) REVERT: G 45 LYS cc_start: 0.8929 (pttt) cc_final: 0.8672 (ptmm) REVERT: G 56 SER cc_start: 0.8351 (m) cc_final: 0.7985 (p) REVERT: I 11 LEU cc_start: 0.5885 (tt) cc_final: 0.5570 (tt) REVERT: M 46 GLU cc_start: 0.8729 (tt0) cc_final: 0.8463 (tt0) REVERT: M 79 SER cc_start: 0.8475 (t) cc_final: 0.8163 (m) REVERT: M 105 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8121 (pt0) REVERT: A 106 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 130 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7894 (tp40) REVERT: A 188 TRP cc_start: 0.7805 (m100) cc_final: 0.7388 (m100) REVERT: A 381 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7594 (mt-10) REVERT: B 577 GLN cc_start: 0.8604 (tp40) cc_final: 0.8392 (tp40) REVERT: B 624 ASP cc_start: 0.8466 (m-30) cc_final: 0.8266 (m-30) REVERT: C 230 ASP cc_start: 0.7701 (t0) cc_final: 0.7445 (t0) REVERT: E 616 ASN cc_start: 0.8654 (t0) cc_final: 0.8448 (p0) REVERT: D 169 ARG cc_start: 0.7388 (mmt90) cc_final: 0.7082 (mtm-85) REVERT: D 230 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: D 232 LYS cc_start: 0.7864 (mttt) cc_final: 0.7614 (mtmm) REVERT: D 314 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7040 (mt0) REVERT: D 325 ASP cc_start: 0.7502 (t0) cc_final: 0.7093 (t0) REVERT: D 335 LYS cc_start: 0.6531 (mttt) cc_final: 0.5988 (pttm) REVERT: D 395 TRP cc_start: 0.7589 (m100) cc_final: 0.7173 (m100) outliers start: 53 outliers final: 40 residues processed: 329 average time/residue: 0.1487 time to fit residues: 77.5155 Evaluate side-chains 328 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 150 optimal weight: 0.5980 chunk 85 optimal weight: 0.0980 chunk 181 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN K 39 GLN N 69 ASN C 167 ASN F 540 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108548 restraints weight = 31164.713| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.92 r_work: 0.3224 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21523 Z= 0.169 Angle : 0.594 19.467 29336 Z= 0.292 Chirality : 0.046 0.427 3446 Planarity : 0.004 0.047 3622 Dihedral : 5.556 58.267 4316 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.99 % Favored : 96.93 % Rotamer: Outliers : 2.76 % Allowed : 12.45 % Favored : 84.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2511 helix: 1.62 (0.28), residues: 386 sheet: 0.45 (0.19), residues: 724 loop : -0.31 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.016 0.002 TYR K 27 PHE 0.012 0.002 PHE A 53 TRP 0.019 0.001 TRP H 103 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00396 (21414) covalent geometry : angle 0.54486 (29044) SS BOND : bond 0.00290 ( 35) SS BOND : angle 0.84089 ( 70) hydrogen bonds : bond 0.03802 ( 612) hydrogen bonds : angle 4.59289 ( 1623) link_BETA1-4 : bond 0.00374 ( 14) link_BETA1-4 : angle 1.86824 ( 42) link_NAG-ASN : bond 0.00441 ( 60) link_NAG-ASN : angle 2.93372 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.7852 (ttp) cc_final: 0.7471 (ttp) REVERT: G 45 LYS cc_start: 0.9190 (pttt) cc_final: 0.8917 (ptmm) REVERT: G 56 SER cc_start: 0.8556 (m) cc_final: 0.8177 (p) REVERT: J 69 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (t0) REVERT: M 2 VAL cc_start: 0.8987 (t) cc_final: 0.8399 (p) REVERT: M 3 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8260 (mp10) REVERT: M 46 GLU cc_start: 0.8844 (tt0) cc_final: 0.8521 (tt0) REVERT: M 79 SER cc_start: 0.8846 (t) cc_final: 0.8523 (m) REVERT: M 105 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8166 (pt0) REVERT: A 106 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: A 130 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7992 (tp40) REVERT: A 188 TRP cc_start: 0.7961 (m100) cc_final: 0.7583 (m100) REVERT: A 381 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7947 (mt-10) REVERT: B 543 ASN cc_start: 0.9066 (m110) cc_final: 0.8861 (m-40) REVERT: B 634 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7878 (tt0) REVERT: B 657 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8841 (mt-10) REVERT: C 120 VAL cc_start: 0.8319 (t) cc_final: 0.8106 (t) REVERT: C 230 ASP cc_start: 0.7972 (t0) cc_final: 0.7606 (t0) REVERT: D 169 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7175 (mtm-85) REVERT: D 199 SER cc_start: 0.7884 (t) cc_final: 0.7148 (p) REVERT: D 230 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: D 232 LYS cc_start: 0.8160 (mttt) cc_final: 0.7938 (mttp) REVERT: D 314 GLN cc_start: 0.7557 (mm-40) cc_final: 0.6955 (mt0) REVERT: D 325 ASP cc_start: 0.7778 (t0) cc_final: 0.7255 (t0) REVERT: D 335 LYS cc_start: 0.6447 (mttt) cc_final: 0.5877 (pttm) REVERT: D 395 TRP cc_start: 0.7529 (m100) cc_final: 0.7039 (m100) outliers start: 61 outliers final: 47 residues processed: 332 average time/residue: 0.1485 time to fit residues: 77.2970 Evaluate side-chains 328 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 163 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 28 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN M 76 ASN N 69 ASN C 167 ASN E 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112535 restraints weight = 31144.684| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.95 r_work: 0.3282 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21523 Z= 0.121 Angle : 0.558 19.581 29336 Z= 0.275 Chirality : 0.044 0.373 3446 Planarity : 0.003 0.044 3622 Dihedral : 5.348 59.674 4316 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 13.31 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2511 helix: 1.78 (0.28), residues: 386 sheet: 0.45 (0.19), residues: 745 loop : -0.31 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 151 TYR 0.014 0.001 TYR K 27 PHE 0.012 0.001 PHE A 53 TRP 0.013 0.001 TRP C 479 HIS 0.003 0.001 HIS I 82A Details of bonding type rmsd covalent geometry : bond 0.00275 (21414) covalent geometry : angle 0.51525 (29044) SS BOND : bond 0.00238 ( 35) SS BOND : angle 0.68895 ( 70) hydrogen bonds : bond 0.03435 ( 612) hydrogen bonds : angle 4.45681 ( 1623) link_BETA1-4 : bond 0.00390 ( 14) link_BETA1-4 : angle 1.81202 ( 42) link_NAG-ASN : bond 0.00476 ( 60) link_NAG-ASN : angle 2.64263 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 67 PHE cc_start: 0.6764 (m-80) cc_final: 0.6226 (m-80) REVERT: L 91 MET cc_start: 0.7868 (ttp) cc_final: 0.7548 (ttp) REVERT: G 56 SER cc_start: 0.8543 (m) cc_final: 0.8179 (p) REVERT: I 11 LEU cc_start: 0.6383 (tt) cc_final: 0.6149 (tt) REVERT: M 46 GLU cc_start: 0.8924 (tt0) cc_final: 0.8640 (tt0) REVERT: M 76 ASN cc_start: 0.8455 (m-40) cc_final: 0.8253 (m110) REVERT: M 79 SER cc_start: 0.8862 (t) cc_final: 0.8588 (m) REVERT: M 105 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8254 (pt0) REVERT: A 106 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: A 130 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8060 (tp40) REVERT: A 188 TRP cc_start: 0.7933 (m100) cc_final: 0.7525 (m100) REVERT: A 381 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7943 (mt-10) REVERT: B 577 GLN cc_start: 0.8506 (tp40) cc_final: 0.8276 (tt0) REVERT: B 634 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7881 (tt0) REVERT: B 657 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8856 (mt-10) REVERT: C 230 ASP cc_start: 0.8034 (t0) cc_final: 0.7720 (t0) REVERT: E 616 ASN cc_start: 0.8896 (t160) cc_final: 0.8620 (p0) REVERT: E 621 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8346 (mt-10) REVERT: D 33 ASN cc_start: 0.8098 (p0) cc_final: 0.7758 (p0) REVERT: D 169 ARG cc_start: 0.7683 (mmt90) cc_final: 0.7247 (mtm-85) REVERT: D 314 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7188 (mt0) REVERT: D 325 ASP cc_start: 0.7478 (t0) cc_final: 0.7029 (t0) REVERT: D 335 LYS cc_start: 0.6547 (mttt) cc_final: 0.6008 (pttm) REVERT: D 395 TRP cc_start: 0.7616 (m100) cc_final: 0.7199 (m100) REVERT: D 449 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7400 (tt) outliers start: 50 outliers final: 37 residues processed: 331 average time/residue: 0.1452 time to fit residues: 76.1482 Evaluate side-chains 316 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 143 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 6 GLN N 69 ASN C 167 ASN E 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107089 restraints weight = 30986.826| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.82 r_work: 0.3209 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21523 Z= 0.196 Angle : 0.615 18.636 29336 Z= 0.302 Chirality : 0.047 0.470 3446 Planarity : 0.004 0.048 3622 Dihedral : 5.587 58.190 4316 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 2.22 % Allowed : 13.58 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2511 helix: 1.61 (0.28), residues: 386 sheet: 0.31 (0.19), residues: 723 loop : -0.39 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 151 TYR 0.016 0.002 TYR N 49 PHE 0.025 0.002 PHE I 67 TRP 0.018 0.002 TRP C 479 HIS 0.006 0.001 HIS I 82A Details of bonding type rmsd covalent geometry : bond 0.00463 (21414) covalent geometry : angle 0.57456 (29044) SS BOND : bond 0.00314 ( 35) SS BOND : angle 0.82706 ( 70) hydrogen bonds : bond 0.03881 ( 612) hydrogen bonds : angle 4.64016 ( 1623) link_BETA1-4 : bond 0.00323 ( 14) link_BETA1-4 : angle 1.87827 ( 42) link_NAG-ASN : bond 0.00531 ( 60) link_NAG-ASN : angle 2.71403 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 288 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 59 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: L 91 MET cc_start: 0.7808 (ttp) cc_final: 0.7427 (ttp) REVERT: G 56 SER cc_start: 0.8723 (m) cc_final: 0.8380 (p) REVERT: M 46 GLU cc_start: 0.8863 (tt0) cc_final: 0.8510 (tt0) REVERT: M 79 SER cc_start: 0.8960 (t) cc_final: 0.8676 (m) REVERT: M 105 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8183 (pt0) REVERT: A 102 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 106 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: A 130 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8009 (tp40) REVERT: A 188 TRP cc_start: 0.7954 (m100) cc_final: 0.7603 (m100) REVERT: A 381 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7956 (mt-10) REVERT: B 543 ASN cc_start: 0.9085 (m110) cc_final: 0.8868 (m-40) REVERT: B 577 GLN cc_start: 0.8550 (tp40) cc_final: 0.8273 (tt0) REVERT: B 634 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7946 (tt0) REVERT: B 657 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8799 (mt-10) REVERT: C 230 ASP cc_start: 0.8036 (t0) cc_final: 0.7638 (t0) REVERT: D 169 ARG cc_start: 0.7634 (mmt90) cc_final: 0.7231 (mtm-85) REVERT: D 314 GLN cc_start: 0.7552 (mm-40) cc_final: 0.6960 (mt0) REVERT: D 325 ASP cc_start: 0.7773 (t0) cc_final: 0.7232 (t0) REVERT: D 335 LYS cc_start: 0.6387 (mttt) cc_final: 0.5814 (pttm) REVERT: D 395 TRP cc_start: 0.7404 (m100) cc_final: 0.6959 (m100) REVERT: D 449 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7316 (tt) REVERT: F 633 LYS cc_start: 0.8109 (mttt) cc_final: 0.7798 (mttm) outliers start: 49 outliers final: 43 residues processed: 321 average time/residue: 0.1423 time to fit residues: 72.3293 Evaluate side-chains 324 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN C 167 ASN E 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107676 restraints weight = 31063.651| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.88 r_work: 0.3226 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21523 Z= 0.158 Angle : 0.587 19.286 29336 Z= 0.288 Chirality : 0.046 0.545 3446 Planarity : 0.003 0.049 3622 Dihedral : 5.503 59.169 4316 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 2.08 % Allowed : 14.12 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.17), residues: 2511 helix: 1.66 (0.28), residues: 386 sheet: 0.29 (0.20), residues: 715 loop : -0.45 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 151 TYR 0.020 0.001 TYR L 89 PHE 0.013 0.001 PHE A 53 TRP 0.016 0.001 TRP C 479 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00372 (21414) covalent geometry : angle 0.54499 (29044) SS BOND : bond 0.00272 ( 35) SS BOND : angle 0.74745 ( 70) hydrogen bonds : bond 0.03673 ( 612) hydrogen bonds : angle 4.56275 ( 1623) link_BETA1-4 : bond 0.00381 ( 14) link_BETA1-4 : angle 1.84234 ( 42) link_NAG-ASN : bond 0.00451 ( 60) link_NAG-ASN : angle 2.67316 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5022 Ramachandran restraints generated. 2511 Oldfield, 0 Emsley, 2511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.7840 (ttp) cc_final: 0.7504 (ttp) REVERT: G 9 SER cc_start: 0.7933 (m) cc_final: 0.7544 (p) REVERT: G 56 SER cc_start: 0.8700 (m) cc_final: 0.8410 (p) REVERT: M 46 GLU cc_start: 0.8877 (tt0) cc_final: 0.8569 (tt0) REVERT: M 79 SER cc_start: 0.8992 (t) cc_final: 0.8744 (m) REVERT: M 105 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8267 (pt0) REVERT: A 106 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 130 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8012 (tp40) REVERT: A 188 TRP cc_start: 0.7975 (m100) cc_final: 0.7582 (m100) REVERT: A 381 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7929 (mt-10) REVERT: B 577 GLN cc_start: 0.8535 (tp40) cc_final: 0.8296 (tt0) REVERT: B 634 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7908 (tt0) REVERT: B 657 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8883 (mt-10) REVERT: C 230 ASP cc_start: 0.8123 (t0) cc_final: 0.7773 (t0) REVERT: D 169 ARG cc_start: 0.7641 (mmt90) cc_final: 0.7308 (mtm-85) REVERT: D 314 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7146 (mt0) REVERT: D 325 ASP cc_start: 0.7723 (t0) cc_final: 0.7169 (t0) REVERT: D 335 LYS cc_start: 0.6526 (mttt) cc_final: 0.5953 (pttm) REVERT: D 395 TRP cc_start: 0.7495 (m100) cc_final: 0.7049 (m100) REVERT: D 449 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7379 (tt) REVERT: F 633 LYS cc_start: 0.8102 (mttt) cc_final: 0.7796 (mttm) outliers start: 46 outliers final: 42 residues processed: 322 average time/residue: 0.1318 time to fit residues: 67.5258 Evaluate side-chains 324 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 97 MET Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain F residue 613 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 23 optimal weight: 0.6980 chunk 183 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 163 optimal weight: 0.0980 chunk 137 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN C 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113198 restraints weight = 30957.356| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.92 r_work: 0.3299 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21523 Z= 0.098 Angle : 0.543 19.351 29336 Z= 0.268 Chirality : 0.044 0.428 3446 Planarity : 0.003 0.048 3622 Dihedral : 5.211 59.903 4316 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 1.45 % Allowed : 15.21 % Favored : 83.34 % 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 aren not related in a simple way. whole: 0.24 (0.17), residues: 2511 helix: 2.00 (0.28), residues: 380 sheet: 0.37 (0.20), residues: 712 loop : -0.44 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 151 TYR 0.014 0.001 TYR K 27 PHE 0.014 0.001 PHE A 53 TRP 0.016 0.001 TRP A 479 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00214 (21414) covalent geometry : angle 0.50131 (29044) SS BOND : bond 0.00193 ( 35) SS BOND : angle 0.64632 ( 70) hydrogen bonds : bond 0.03239 ( 612) hydrogen bonds : angle 4.40697 ( 1623) link_BETA1-4 : bond 0.00463 ( 14) link_BETA1-4 : angle 1.76119 ( 42) link_NAG-ASN : bond 0.00477 ( 60) link_NAG-ASN : angle 2.56361 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6074.31 seconds wall clock time: 104 minutes 39.04 seconds (6279.04 seconds total)