Starting phenix.real_space_refine on Mon Aug 25 07:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw4_40797/08_2025/8sw4_40797.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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 160 5.16 5 C 16508 2.51 5 N 4493 2.21 5 O 5162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 26323 Number of models: 1 Model: "" Number of chains: 30 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 4 Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 928 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3452 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 4 Chain: "G" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" 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: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 4 Chain: "I" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" 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: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "O" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1002 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "P" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "Q" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1012 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "S" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "T" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.18 Number of scatterers: 26323 At special positions: 0 Unit cell: (141.984, 140.94, 148.248, 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 160 16.00 O 5162 8.00 N 4493 7.00 C 16508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.01 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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 296 " - pdb=" SG CYS A 331 " 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=1.80 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=1.60 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " 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 I 605 " distance=2.02 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.02 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 601 " - " ASN A 156 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 156 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 392 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 295 " " NAG D 604 " - " ASN D 301 " " NAG D 605 " - " ASN D 332 " " NAG D 606 " - " ASN D 363 " " NAG D 607 " - " ASN D 448 " " NAG D 608 " - " ASN D 88 " " NAG D 609 " - " ASN D 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG I 701 " - " ASN I 618 " " NAG I 702 " - " ASN I 637 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN D 262 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 692.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6034 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 53 sheets defined 17.1% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.772A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.031A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.855A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.560A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.441A 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 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.631A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.638A pdb=" N THR E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.016A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.086A 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 335 through 354 removed outlier: 3.890A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.207A 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: 4.058A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.384A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 Processing helix chain 'G' and resid 572 through 596 Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 662 removed outlier: 3.648A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.540A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.633A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.101A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.578A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.781A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.359A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.722A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 596 Processing helix chain 'I' and resid 618 through 622 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 650 removed outlier: 3.579A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 652 through 662 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.978A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 31 removed outlier: 3.967A pdb=" N PHE O 29 " --> pdb=" O ASP O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 27 through 31 removed outlier: 3.624A pdb=" N GLY Q 30 " --> pdb=" O ASP Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.801A pdb=" N PHE S 29 " --> pdb=" O ASP S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 65 No H-bonds generated for 'chain 'S' and resid 63 through 65' Processing helix chain 'S' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100I through 103 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'L' and resid 33 through 38 removed outlier: 6.424A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.320A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.716A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.814A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 4.212A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.899A pdb=" N MET E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 59 current: chain 'E' and resid 100H through 103 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 11 through 12 current: chain 'F' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 48 current: chain 'F' and resid 95A through 98 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL G 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL C 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR G 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR C 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N CYS G 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.651A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.676A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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 302 removed outlier: 4.024A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 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=AC6, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.503A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AC8, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC9, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.382A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 Processing sheet with id=AD2, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.490A pdb=" N VAL D 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.562A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.951A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 302 removed outlier: 4.065A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 322 through 323 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AD9, first strand: chain 'D' and resid 305 through 312 removed outlier: 7.154A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.857A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 94 through 95 removed outlier: 3.794A pdb=" N PHE K 102 " --> pdb=" O THR K 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.256A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) 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 Processing sheet with id=AE6, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'O' and resid 34 through 39 removed outlier: 7.090A pdb=" N PHE O 34 " --> pdb=" O ALA O 52 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA O 52 " --> pdb=" O PHE O 34 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TRP O 35A" --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR O 50 " --> pdb=" O TRP O 35A" (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 102 through 103 Processing sheet with id=AE8, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'P' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 12 current: chain 'P' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 53 through 54 current: chain 'P' and resid 97 through 98 Processing sheet with id=AF1, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 12 current: chain 'Q' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 59 current: chain 'Q' and resid 102 through 103 Processing sheet with id=AF3, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 13 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'S' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 11 through 12 current: chain 'S' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 45 through 52 current: chain 'S' and resid 102 through 103 No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.490A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1842 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: 3.78 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7568 1.33 - 1.46: 7214 1.46 - 1.59: 11886 1.59 - 1.71: 2 1.71 - 1.84: 220 Bond restraints: 26890 Sorted by residual: bond pdb=" C1 NAG G 702 " pdb=" O5 NAG G 702 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" N CYS A 54 " pdb=" CA CYS A 54 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N TYR R 49 " pdb=" CA TYR R 49 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.35e-02 5.49e+03 8.98e+00 ... (remaining 26885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 34094 2.20 - 4.40: 2068 4.40 - 6.60: 286 6.60 - 8.80: 38 8.80 - 11.00: 8 Bond angle restraints: 36494 Sorted by residual: angle pdb=" N LEU G 663 " pdb=" CA LEU G 663 " pdb=" C LEU G 663 " ideal model delta sigma weight residual 114.04 106.59 7.45 1.24e+00 6.50e-01 3.61e+01 angle pdb=" O TYR D 217 " pdb=" C TYR D 217 " pdb=" N CYS D 218 " ideal model delta sigma weight residual 123.27 127.78 -4.51 1.13e+00 7.83e-01 1.59e+01 angle pdb=" CA TYR M 49 " pdb=" CB TYR M 49 " pdb=" CG TYR M 49 " ideal model delta sigma weight residual 113.90 121.04 -7.14 1.80e+00 3.09e-01 1.57e+01 angle pdb=" CA GLN L 100 " pdb=" CB GLN L 100 " pdb=" CG GLN L 100 " ideal model delta sigma weight residual 114.10 121.99 -7.89 2.00e+00 2.50e-01 1.56e+01 angle pdb=" N VAL B 570 " pdb=" CA VAL B 570 " pdb=" C VAL B 570 " ideal model delta sigma weight residual 110.62 106.62 4.00 1.02e+00 9.61e-01 1.54e+01 ... (remaining 36489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 15751 23.47 - 46.93: 624 46.93 - 70.40: 154 70.40 - 93.86: 45 93.86 - 117.33: 15 Dihedral angle restraints: 16589 sinusoidal: 7137 harmonic: 9452 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 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 36.26 56.74 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 92 " pdb=" CB CYS S 92 " ideal model delta sinusoidal sigma weight residual 93.00 149.10 -56.10 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 16586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 4160 0.316 - 0.633: 3 0.633 - 0.949: 0 0.949 - 1.266: 0 1.266 - 1.582: 1 Chirality restraints: 4164 Sorted by residual: chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 448 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG G 702 " pdb=" ND2 ASN G 618 " pdb=" C2 NAG G 702 " pdb=" O5 NAG G 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CG LEU B 660 " pdb=" CB LEU B 660 " pdb=" CD1 LEU B 660 " pdb=" CD2 LEU B 660 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4161 not shown) Planarity restraints: 4643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 652 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" CD GLN B 652 " 0.075 2.00e-02 2.50e+03 pdb=" OE1 GLN B 652 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 GLN B 652 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP S 26 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASP S 26 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP S 26 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP S 27 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C ARG A 476 " -0.068 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.023 2.00e-02 2.50e+03 ... (remaining 4640 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 208 2.59 - 3.17: 21420 3.17 - 3.74: 40744 3.74 - 4.32: 62168 4.32 - 4.90: 100322 Nonbonded interactions: 224862 Sorted by model distance: nonbonded pdb=" OG SER M 14 " pdb=" OE1 GLN M 17 " model vdw 2.012 3.040 nonbonded pdb=" O SER S 32 " pdb=" OH TYR S 100C" model vdw 2.030 3.040 nonbonded pdb=" OD1 ASN A 99 " pdb=" NE2 GLN A 103 " model vdw 2.089 3.120 nonbonded pdb=" NZ LYS C 207 " pdb=" OD2 ASP O 27 " model vdw 2.166 3.120 nonbonded pdb=" OG SER N 12 " pdb=" OG1 THR N 105 " model vdw 2.181 3.040 ... (remaining 224857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 459 or resid 464 through 503 or resid 601 throu \ gh 608)) selection = (chain 'C' and (resid 33 through 57 or resid 71 through 398 or resid 412 through \ 459 or resid 464 through 503 or resid 602 through 609)) selection = (chain 'D' and (resid 33 through 57 or resid 71 through 398 or resid 412 through \ 503 or resid 602 through 609)) } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 570 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)) or resid 701 through 702)) selection = chain 'G' selection = (chain 'I' and (resid 520 through 546 or resid 570 through 702)) } ncs_group { reference = chain 'E' selection = (chain 'J' and resid 2 through 111) selection = (chain 'K' and resid 2 through 111) } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'O' and resid 2 through 111) selection = (chain 'Q' and resid 2 through 111) selection = (chain 'S' and resid 2 through 111) } ncs_group { reference = chain 'P' selection = (chain 'R' and resid 1 through 106) selection = (chain 'T' and resid 1 through 106) } ncs_group { reference = chain 'U' selection = chain 'W' 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.540 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.008 0.428 26984 Z= 0.354 Angle : 1.205 29.186 36729 Z= 0.669 Chirality : 0.070 1.582 4164 Planarity : 0.006 0.055 4606 Dihedral : 13.704 117.329 10414 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.45 (0.14), residues: 3233 helix: -0.47 (0.24), residues: 402 sheet: 0.60 (0.15), residues: 1086 loop : 0.44 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG N 103 TYR 0.045 0.004 TYR Q 50 PHE 0.037 0.003 PHE C 210 TRP 0.025 0.003 TRP O 47 HIS 0.022 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00722 (26890) covalent geometry : angle 1.16545 (36494) SS BOND : bond 0.07165 ( 47) SS BOND : angle 4.86517 ( 94) hydrogen bonds : bond 0.12670 ( 726) hydrogen bonds : angle 7.04841 ( 1842) link_ALPHA1-3 : bond 0.00584 ( 3) link_ALPHA1-3 : angle 0.96961 ( 9) link_BETA1-4 : bond 0.01016 ( 7) link_BETA1-4 : angle 3.69643 ( 21) link_NAG-ASN : bond 0.00585 ( 37) link_NAG-ASN : angle 3.39598 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 525 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 82 ASP cc_start: 0.7539 (m-30) cc_final: 0.7271 (m-30) REVERT: A 141 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6354 (p0) REVERT: A 232 LYS cc_start: 0.8061 (mttt) cc_final: 0.7265 (tmtt) REVERT: A 347 LYS cc_start: 0.8426 (tttt) cc_final: 0.8221 (ttmp) REVERT: F 45 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8258 (ttpt) REVERT: F 103 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7476 (mtp85) REVERT: C 136 ASN cc_start: 0.6892 (m-40) cc_final: 0.5472 (p0) REVERT: G 641 ILE cc_start: 0.8639 (mt) cc_final: 0.8385 (mt) REVERT: D 46 LYS cc_start: 0.8579 (mttm) cc_final: 0.8180 (mttm) REVERT: D 246 GLN cc_start: 0.7861 (pm20) cc_final: 0.7014 (tp40) REVERT: I 616 ASN cc_start: 0.8544 (t0) cc_final: 0.8281 (t0) REVERT: K 81 GLN cc_start: 0.8275 (tp40) cc_final: 0.7961 (tp-100) REVERT: K 100 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8322 (ttmp) REVERT: N 6 GLN cc_start: 0.7248 (mt0) cc_final: 0.6908 (mt0) REVERT: N 30 TYR cc_start: 0.8786 (m-80) cc_final: 0.8478 (m-80) REVERT: O 73 ILE cc_start: 0.8622 (mm) cc_final: 0.8412 (mm) REVERT: P 87 TYR cc_start: 0.8352 (m-80) cc_final: 0.8139 (m-80) REVERT: Q 100 TYR cc_start: 0.8568 (m-80) cc_final: 0.8068 (m-80) outliers start: 4 outliers final: 2 residues processed: 529 average time/residue: 0.5569 time to fit residues: 339.3587 Evaluate side-chains 453 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 450 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain Q residue 73 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN A 103 GLN A 302 ASN A 315 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN F 38 GLN F 79 GLN C 114 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 630 GLN J 81 GLN M 17 GLN M 53 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN I 652 GLN I 656 ASN N 39 HIS P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 HIS S 3 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112092 restraints weight = 31308.178| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.90 r_work: 0.3138 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26984 Z= 0.203 Angle : 0.647 16.209 36729 Z= 0.333 Chirality : 0.048 0.492 4164 Planarity : 0.005 0.041 4606 Dihedral : 7.582 75.085 4559 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.00 % Allowed : 10.43 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.41 (0.14), residues: 3233 helix: 0.49 (0.27), residues: 408 sheet: 0.29 (0.15), residues: 1113 loop : 0.37 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 327 TYR 0.025 0.002 TYR Q 50 PHE 0.020 0.002 PHE O 78 TRP 0.023 0.002 TRP K 103 HIS 0.006 0.001 HIS Q 74 Details of bonding type rmsd covalent geometry : bond 0.00478 (26890) covalent geometry : angle 0.62237 (36494) SS BOND : bond 0.00507 ( 47) SS BOND : angle 1.09440 ( 94) hydrogen bonds : bond 0.04711 ( 726) hydrogen bonds : angle 5.70550 ( 1842) link_ALPHA1-3 : bond 0.00872 ( 3) link_ALPHA1-3 : angle 2.38275 ( 9) link_BETA1-4 : bond 0.00679 ( 7) link_BETA1-4 : angle 2.65663 ( 21) link_NAG-ASN : bond 0.00461 ( 37) link_NAG-ASN : angle 2.87202 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 453 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8583 (pt0) cc_final: 0.8157 (pt0) REVERT: H 18 LEU cc_start: 0.8003 (mt) cc_final: 0.7618 (mt) REVERT: H 46 GLU cc_start: 0.8625 (tt0) cc_final: 0.8416 (tt0) REVERT: H 53 TYR cc_start: 0.8623 (p90) cc_final: 0.8352 (p90) REVERT: H 83 ARG cc_start: 0.7399 (ptp-170) cc_final: 0.6792 (ptp90) REVERT: H 94 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8437 (ttpt) REVERT: L 91 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8694 (ptm160) REVERT: A 141 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6480 (p0) REVERT: A 232 LYS cc_start: 0.8368 (mttt) cc_final: 0.6973 (tmtt) REVERT: A 347 LYS cc_start: 0.8627 (tttt) cc_final: 0.8266 (ttmt) REVERT: B 647 GLU cc_start: 0.7963 (tt0) cc_final: 0.7637 (tt0) REVERT: B 664 ASP cc_start: 0.7061 (m-30) cc_final: 0.6814 (m-30) REVERT: E 3 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: E 19 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8098 (ttmt) REVERT: E 39 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: F 42 LYS cc_start: 0.7546 (mttp) cc_final: 0.6577 (mmtt) REVERT: F 81 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7286 (p0) REVERT: F 103 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7318 (mtp85) REVERT: C 136 ASN cc_start: 0.6535 (m-40) cc_final: 0.5620 (p0) REVERT: C 161 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7294 (ttp) REVERT: G 641 ILE cc_start: 0.8781 (mt) cc_final: 0.8523 (mt) REVERT: D 46 LYS cc_start: 0.8721 (mttm) cc_final: 0.8281 (mttm) REVERT: D 231 LYS cc_start: 0.8236 (mttt) cc_final: 0.8015 (mppt) REVERT: I 632 ASP cc_start: 0.8308 (t0) cc_final: 0.7763 (t0) REVERT: I 633 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7661 (mtpt) REVERT: K 100 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8445 (ttmp) REVERT: N 30 TYR cc_start: 0.8897 (m-80) cc_final: 0.8572 (m-80) REVERT: N 85 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: O 11 ARG cc_start: 0.6097 (mtp85) cc_final: 0.5766 (mmt-90) REVERT: P 3 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: P 106 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4804 (pp) REVERT: Q 100 TYR cc_start: 0.8413 (m-80) cc_final: 0.8101 (m-80) REVERT: S 27 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8082 (m-30) outliers start: 85 outliers final: 40 residues processed: 496 average time/residue: 0.5491 time to fit residues: 314.7014 Evaluate side-chains 458 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 408 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 106 ILE Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 198 optimal weight: 3.9990 chunk 197 optimal weight: 0.0570 chunk 138 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS L 27 GLN A 33 ASN A 315 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN M 53 GLN M 69 ASN D 283 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 630 GLN I 656 ASN K 81 GLN K 82AHIS P 28 ASN P 31 ASN Q 60 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN T 31 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109532 restraints weight = 31548.009| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3142 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26984 Z= 0.213 Angle : 0.621 15.577 36729 Z= 0.317 Chirality : 0.047 0.444 4164 Planarity : 0.004 0.045 4606 Dihedral : 6.666 62.581 4559 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.63 % Allowed : 11.24 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.29 (0.14), residues: 3233 helix: 0.52 (0.27), residues: 413 sheet: 0.19 (0.15), residues: 1082 loop : 0.26 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 81 TYR 0.023 0.002 TYR R 49 PHE 0.021 0.002 PHE O 78 TRP 0.016 0.002 TRP H 103 HIS 0.005 0.001 HIS O 74 Details of bonding type rmsd covalent geometry : bond 0.00508 (26890) covalent geometry : angle 0.59895 (36494) SS BOND : bond 0.00516 ( 47) SS BOND : angle 1.35878 ( 94) hydrogen bonds : bond 0.04459 ( 726) hydrogen bonds : angle 5.40930 ( 1842) link_ALPHA1-3 : bond 0.00956 ( 3) link_ALPHA1-3 : angle 1.62335 ( 9) link_BETA1-4 : bond 0.00700 ( 7) link_BETA1-4 : angle 1.97924 ( 21) link_NAG-ASN : bond 0.00476 ( 37) link_NAG-ASN : angle 2.63644 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 429 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8596 (pt0) cc_final: 0.8185 (pt0) REVERT: H 83 ARG cc_start: 0.7420 (ptp-170) cc_final: 0.6941 (ptp-170) REVERT: H 94 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8426 (ttpt) REVERT: L 91 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8807 (ptm160) REVERT: A 103 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: A 126 CYS cc_start: 0.7889 (t) cc_final: 0.7547 (t) REVERT: A 141 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6565 (p0) REVERT: A 232 LYS cc_start: 0.8560 (mttt) cc_final: 0.7260 (tmtt) REVERT: A 347 LYS cc_start: 0.8664 (tttt) cc_final: 0.8366 (ttmt) REVERT: B 574 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7560 (mtpp) REVERT: B 647 GLU cc_start: 0.8090 (tt0) cc_final: 0.7810 (tt0) REVERT: E 19 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8239 (ttmt) REVERT: F 42 LYS cc_start: 0.7842 (mttp) cc_final: 0.6940 (mmtt) REVERT: F 81 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7370 (p0) REVERT: F 103 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7541 (mtp85) REVERT: C 114 GLN cc_start: 0.8217 (pt0) cc_final: 0.7937 (pt0) REVERT: C 136 ASN cc_start: 0.6732 (m-40) cc_final: 0.5898 (p0) REVERT: C 232 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7945 (mtpp) REVERT: G 626 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8848 (ttp) REVERT: G 641 ILE cc_start: 0.8909 (mt) cc_final: 0.8676 (mt) REVERT: J 23 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (mmm160) REVERT: D 46 LYS cc_start: 0.8712 (mttm) cc_final: 0.8433 (mttm) REVERT: D 138 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7111 (pp) REVERT: I 633 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7767 (mtpt) REVERT: I 657 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: I 661 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8304 (tp) REVERT: K 100 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8512 (tttp) REVERT: N 30 TYR cc_start: 0.8982 (m-80) cc_final: 0.8762 (m-80) REVERT: O 11 ARG cc_start: 0.6077 (mtp85) cc_final: 0.5769 (mmt-90) REVERT: P 3 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8057 (mt0) outliers start: 103 outliers final: 50 residues processed: 485 average time/residue: 0.5573 time to fit residues: 313.0940 Evaluate side-chains 467 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 91 ARG Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 229 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 279 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 274 optimal weight: 0.7980 chunk 168 optimal weight: 0.0270 chunk 268 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 103 GLN A 315 GLN B 607 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 656 ASN K 81 GLN K 82AHIS N 31 ASN P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN T 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111694 restraints weight = 31446.612| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.01 r_work: 0.3174 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26984 Z= 0.129 Angle : 0.539 14.503 36729 Z= 0.274 Chirality : 0.044 0.403 4164 Planarity : 0.004 0.069 4606 Dihedral : 5.786 51.306 4559 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.75 % Allowed : 13.07 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.34 (0.15), residues: 3233 helix: 0.72 (0.27), residues: 413 sheet: 0.19 (0.15), residues: 1077 loop : 0.27 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 56 TYR 0.016 0.001 TYR Q 50 PHE 0.019 0.002 PHE O 78 TRP 0.013 0.001 TRP K 103 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00302 (26890) covalent geometry : angle 0.51767 (36494) SS BOND : bond 0.00357 ( 47) SS BOND : angle 1.11335 ( 94) hydrogen bonds : bond 0.03739 ( 726) hydrogen bonds : angle 5.13356 ( 1842) link_ALPHA1-3 : bond 0.01035 ( 3) link_ALPHA1-3 : angle 1.80655 ( 9) link_BETA1-4 : bond 0.00648 ( 7) link_BETA1-4 : angle 1.63635 ( 21) link_NAG-ASN : bond 0.00376 ( 37) link_NAG-ASN : angle 2.48742 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 423 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8653 (pt0) cc_final: 0.8264 (pt0) REVERT: H 83 ARG cc_start: 0.7404 (ptp-170) cc_final: 0.6911 (ptp-170) REVERT: H 94 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8378 (ttpt) REVERT: A 126 CYS cc_start: 0.7829 (t) cc_final: 0.7488 (t) REVERT: A 141 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6570 (p0) REVERT: A 232 LYS cc_start: 0.8622 (mttt) cc_final: 0.7412 (tmtt) REVERT: A 347 LYS cc_start: 0.8672 (tttt) cc_final: 0.8360 (ttmt) REVERT: B 574 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7542 (mtpp) REVERT: B 647 GLU cc_start: 0.7879 (tt0) cc_final: 0.7574 (tt0) REVERT: F 42 LYS cc_start: 0.7842 (mttp) cc_final: 0.6914 (mmtt) REVERT: F 81 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7382 (p0) REVERT: C 116 LEU cc_start: 0.8431 (mt) cc_final: 0.8206 (mm) REVERT: C 136 ASN cc_start: 0.6683 (m-40) cc_final: 0.5984 (p0) REVERT: C 232 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7976 (mtpp) REVERT: G 641 ILE cc_start: 0.8858 (mt) cc_final: 0.8611 (mt) REVERT: G 655 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7777 (mtmm) REVERT: J 23 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7594 (mmm160) REVERT: J 32 PHE cc_start: 0.8325 (m-80) cc_final: 0.7829 (m-80) REVERT: J 38 ARG cc_start: 0.8701 (ptt180) cc_final: 0.8405 (ptt180) REVERT: M 45 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7944 (ttmm) REVERT: M 53 GLN cc_start: 0.7844 (mm110) cc_final: 0.7402 (mm110) REVERT: M 85 ASP cc_start: 0.7664 (m-30) cc_final: 0.7416 (m-30) REVERT: D 46 LYS cc_start: 0.8700 (mttm) cc_final: 0.8213 (mttm) REVERT: D 231 LYS cc_start: 0.8424 (mttt) cc_final: 0.8149 (mppt) REVERT: D 492 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8033 (mt-10) REVERT: I 588 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7629 (mtm-85) REVERT: I 633 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7705 (mtpt) REVERT: I 657 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: I 661 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7968 (tp) REVERT: K 100 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8485 (tttp) REVERT: N 30 TYR cc_start: 0.8968 (m-80) cc_final: 0.8682 (m-80) REVERT: O 11 ARG cc_start: 0.6039 (mtp85) cc_final: 0.5715 (mmt-90) REVERT: T 103 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7325 (tmm) REVERT: T 106 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6257 (mt) outliers start: 78 outliers final: 40 residues processed: 471 average time/residue: 0.6112 time to fit residues: 332.6496 Evaluate side-chains 452 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 404 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 103 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 656 ASN P 28 ASN P 31 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 HIS S 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109622 restraints weight = 31552.552| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.92 r_work: 0.3130 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26984 Z= 0.173 Angle : 0.566 14.416 36729 Z= 0.287 Chirality : 0.045 0.403 4164 Planarity : 0.004 0.059 4606 Dihedral : 5.456 52.274 4557 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.45 % Allowed : 12.90 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.27 (0.15), residues: 3233 helix: 0.84 (0.27), residues: 400 sheet: 0.13 (0.15), residues: 1083 loop : 0.19 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 56 TYR 0.021 0.002 TYR Q 50 PHE 0.020 0.002 PHE O 78 TRP 0.015 0.002 TRP S 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00415 (26890) covalent geometry : angle 0.54706 (36494) SS BOND : bond 0.00412 ( 47) SS BOND : angle 1.18555 ( 94) hydrogen bonds : bond 0.03924 ( 726) hydrogen bonds : angle 5.10270 ( 1842) link_ALPHA1-3 : bond 0.00976 ( 3) link_ALPHA1-3 : angle 1.65640 ( 9) link_BETA1-4 : bond 0.00613 ( 7) link_BETA1-4 : angle 1.67627 ( 21) link_NAG-ASN : bond 0.00444 ( 37) link_NAG-ASN : angle 2.37735 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 412 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8688 (pt0) cc_final: 0.8293 (pt0) REVERT: H 83 ARG cc_start: 0.7422 (ptp-170) cc_final: 0.6909 (ptp90) REVERT: H 94 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8552 (ttpt) REVERT: A 126 CYS cc_start: 0.7926 (t) cc_final: 0.7593 (t) REVERT: A 232 LYS cc_start: 0.8652 (mttt) cc_final: 0.7438 (tmtt) REVERT: A 347 LYS cc_start: 0.8755 (tttt) cc_final: 0.8423 (ttmt) REVERT: B 574 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7565 (mtpp) REVERT: B 647 GLU cc_start: 0.8076 (tt0) cc_final: 0.7813 (tt0) REVERT: B 650 GLN cc_start: 0.5859 (tt0) cc_final: 0.5545 (tt0) REVERT: F 27 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7626 (mm) REVERT: F 81 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7317 (p0) REVERT: C 116 LEU cc_start: 0.8508 (mt) cc_final: 0.8287 (mm) REVERT: C 136 ASN cc_start: 0.6625 (m-40) cc_final: 0.5775 (p0) REVERT: C 192 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7576 (ttp-110) REVERT: C 232 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (mmpt) REVERT: G 641 ILE cc_start: 0.8907 (mt) cc_final: 0.8659 (mt) REVERT: J 23 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7726 (mmm160) REVERT: J 32 PHE cc_start: 0.8387 (m-80) cc_final: 0.7881 (m-80) REVERT: M 53 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7508 (mm110) REVERT: M 85 ASP cc_start: 0.7678 (m-30) cc_final: 0.7440 (m-30) REVERT: D 46 LYS cc_start: 0.8695 (mttm) cc_final: 0.8434 (mttm) REVERT: D 99 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8260 (p0) REVERT: D 138 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7141 (pp) REVERT: D 246 GLN cc_start: 0.7912 (pm20) cc_final: 0.6831 (tp40) REVERT: D 424 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8051 (pt) REVERT: I 588 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7724 (mtm-85) REVERT: I 633 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7761 (mtpt) REVERT: I 657 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: I 661 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (tp) REVERT: N 30 TYR cc_start: 0.9003 (m-80) cc_final: 0.8732 (m-80) REVERT: P 3 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: T 106 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6327 (mt) outliers start: 98 outliers final: 53 residues processed: 471 average time/residue: 0.5646 time to fit residues: 308.5756 Evaluate side-chains 464 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 399 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 639 THR Chi-restraints excluded: chain I residue 648 GLU Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 82 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 0.0570 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 103 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN C 216 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 656 ASN K 82AHIS P 28 ASN P 79 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108135 restraints weight = 31586.589| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.92 r_work: 0.3110 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26984 Z= 0.202 Angle : 0.583 14.600 36729 Z= 0.296 Chirality : 0.046 0.408 4164 Planarity : 0.004 0.055 4606 Dihedral : 5.406 52.412 4555 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.45 % Allowed : 13.11 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.10 (0.15), residues: 3233 helix: 0.72 (0.27), residues: 400 sheet: 0.00 (0.15), residues: 1086 loop : 0.09 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 56 TYR 0.023 0.002 TYR R 49 PHE 0.021 0.002 PHE O 78 TRP 0.016 0.002 TRP S 47 HIS 0.004 0.001 HIS O 74 Details of bonding type rmsd covalent geometry : bond 0.00485 (26890) covalent geometry : angle 0.56407 (36494) SS BOND : bond 0.00449 ( 47) SS BOND : angle 1.22769 ( 94) hydrogen bonds : bond 0.04048 ( 726) hydrogen bonds : angle 5.15255 ( 1842) link_ALPHA1-3 : bond 0.00903 ( 3) link_ALPHA1-3 : angle 1.69903 ( 9) link_BETA1-4 : bond 0.00598 ( 7) link_BETA1-4 : angle 1.61728 ( 21) link_NAG-ASN : bond 0.00502 ( 37) link_NAG-ASN : angle 2.45554 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 404 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8697 (pt0) cc_final: 0.8292 (pt0) REVERT: H 83 ARG cc_start: 0.7440 (ptp-170) cc_final: 0.6930 (ptp90) REVERT: H 94 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8368 (ttpt) REVERT: A 126 CYS cc_start: 0.7960 (t) cc_final: 0.7619 (t) REVERT: A 232 LYS cc_start: 0.8636 (mttt) cc_final: 0.7396 (tmtt) REVERT: A 347 LYS cc_start: 0.8751 (tttt) cc_final: 0.8399 (ttmt) REVERT: B 574 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7516 (mtpp) REVERT: B 647 GLU cc_start: 0.8091 (tt0) cc_final: 0.7831 (tt0) REVERT: F 27 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7611 (mm) REVERT: F 42 LYS cc_start: 0.7933 (mttp) cc_final: 0.7033 (mmtt) REVERT: F 81 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7314 (p0) REVERT: F 103 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7427 (mtp85) REVERT: C 116 LEU cc_start: 0.8489 (mt) cc_final: 0.8287 (mm) REVERT: C 136 ASN cc_start: 0.6716 (m-40) cc_final: 0.5839 (p0) REVERT: C 192 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7335 (ttp-110) REVERT: C 232 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7951 (mtpp) REVERT: C 490 LYS cc_start: 0.8882 (pttt) cc_final: 0.8380 (ptmt) REVERT: G 535 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8334 (mpp) REVERT: G 641 ILE cc_start: 0.8891 (mt) cc_final: 0.8643 (mt) REVERT: J 23 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7591 (mmm160) REVERT: J 32 PHE cc_start: 0.8430 (m-80) cc_final: 0.7934 (m-80) REVERT: M 85 ASP cc_start: 0.7766 (m-30) cc_final: 0.7533 (m-30) REVERT: D 46 LYS cc_start: 0.8707 (mttm) cc_final: 0.8444 (mttm) REVERT: D 99 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8211 (p0) REVERT: D 138 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7210 (pp) REVERT: D 269 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6645 (tp30) REVERT: D 424 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8108 (pt) REVERT: I 588 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7696 (mtm-85) REVERT: I 612 SER cc_start: 0.8699 (m) cc_final: 0.8429 (t) REVERT: I 633 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7706 (mtpt) REVERT: I 657 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: I 661 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8190 (tp) REVERT: K 100 LYS cc_start: 0.8832 (tttp) cc_final: 0.8518 (tttt) REVERT: N 30 TYR cc_start: 0.9011 (m-80) cc_final: 0.8733 (m-80) REVERT: O 46 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: P 3 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: T 103 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: T 106 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6276 (mt) outliers start: 98 outliers final: 59 residues processed: 460 average time/residue: 0.5749 time to fit residues: 306.6022 Evaluate side-chains 475 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain G residue 535 MET Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 639 THR Chi-restraints excluded: chain I residue 648 GLU Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 80 SER Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 299 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 184 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 99 ASN A 103 GLN B 577 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN E 76 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 625 ASN I 656 ASN O 5 GLN O 95 HIS P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107604 restraints weight = 31573.711| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.93 r_work: 0.3099 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26984 Z= 0.202 Angle : 0.582 14.588 36729 Z= 0.295 Chirality : 0.046 0.412 4164 Planarity : 0.004 0.052 4606 Dihedral : 5.437 52.454 4555 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.70 % Allowed : 13.53 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.01 (0.15), residues: 3233 helix: 0.74 (0.27), residues: 398 sheet: -0.10 (0.15), residues: 1091 loop : 0.04 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 56 TYR 0.024 0.002 TYR R 49 PHE 0.021 0.002 PHE O 78 TRP 0.018 0.002 TRP S 47 HIS 0.004 0.001 HIS Q 95 Details of bonding type rmsd covalent geometry : bond 0.00485 (26890) covalent geometry : angle 0.56316 (36494) SS BOND : bond 0.00462 ( 47) SS BOND : angle 1.20721 ( 94) hydrogen bonds : bond 0.04050 ( 726) hydrogen bonds : angle 5.15902 ( 1842) link_ALPHA1-3 : bond 0.00872 ( 3) link_ALPHA1-3 : angle 1.65174 ( 9) link_BETA1-4 : bond 0.00592 ( 7) link_BETA1-4 : angle 1.56008 ( 21) link_NAG-ASN : bond 0.00486 ( 37) link_NAG-ASN : angle 2.45946 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 411 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8691 (pt0) cc_final: 0.8292 (pt0) REVERT: H 83 ARG cc_start: 0.7418 (ptp-170) cc_final: 0.7192 (ptp-170) REVERT: H 94 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8361 (ttpt) REVERT: A 103 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: A 126 CYS cc_start: 0.8023 (t) cc_final: 0.7670 (t) REVERT: A 232 LYS cc_start: 0.8647 (mttt) cc_final: 0.7426 (tmtt) REVERT: A 347 LYS cc_start: 0.8764 (tttt) cc_final: 0.8393 (ttmt) REVERT: B 574 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7551 (mtpp) REVERT: F 27 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7539 (mm) REVERT: F 42 LYS cc_start: 0.7900 (mttp) cc_final: 0.6985 (mmtt) REVERT: F 81 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7308 (p0) REVERT: F 103 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7431 (mtp85) REVERT: C 116 LEU cc_start: 0.8535 (mt) cc_final: 0.8305 (mm) REVERT: C 136 ASN cc_start: 0.6677 (m-40) cc_final: 0.5905 (p0) REVERT: C 192 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7332 (ttp-110) REVERT: C 232 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7952 (mtpp) REVERT: C 424 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8075 (pt) REVERT: C 490 LYS cc_start: 0.8872 (pttt) cc_final: 0.8369 (ptmt) REVERT: G 641 ILE cc_start: 0.8919 (mt) cc_final: 0.8676 (mt) REVERT: J 23 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7552 (mmm160) REVERT: J 32 PHE cc_start: 0.8481 (m-80) cc_final: 0.7965 (m-80) REVERT: J 38 ARG cc_start: 0.8655 (ptt180) cc_final: 0.8413 (ptt180) REVERT: M 85 ASP cc_start: 0.7757 (m-30) cc_final: 0.7547 (m-30) REVERT: D 46 LYS cc_start: 0.8729 (mttm) cc_final: 0.8485 (mttm) REVERT: D 99 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8175 (p0) REVERT: D 138 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7271 (pp) REVERT: D 246 GLN cc_start: 0.7912 (pm20) cc_final: 0.6844 (tp40) REVERT: D 424 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8102 (pt) REVERT: I 535 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8036 (mpt) REVERT: I 588 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7635 (mtm180) REVERT: I 612 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8446 (t) REVERT: I 633 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7754 (mtpt) REVERT: I 657 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: I 661 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (tp) REVERT: K 100 LYS cc_start: 0.8817 (tttp) cc_final: 0.8460 (ttmt) REVERT: N 30 TYR cc_start: 0.9010 (m-80) cc_final: 0.8759 (m-80) REVERT: O 46 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: P 3 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: P 42 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8257 (mmmm) REVERT: S 105 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: T 70 ASP cc_start: 0.7720 (m-30) cc_final: 0.7485 (m-30) REVERT: T 103 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7339 (tmm) REVERT: T 106 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6270 (mt) outliers start: 105 outliers final: 63 residues processed: 469 average time/residue: 0.5992 time to fit residues: 324.8545 Evaluate side-chains 478 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 396 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 639 THR Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 80 SER Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 50 TYR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 285 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 196 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 103 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 625 ASN I 656 ASN K 82AHIS P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107369 restraints weight = 31722.417| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.88 r_work: 0.3097 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26984 Z= 0.207 Angle : 0.587 14.550 36729 Z= 0.297 Chirality : 0.046 0.409 4164 Planarity : 0.004 0.057 4606 Dihedral : 5.469 52.491 4555 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.56 % Allowed : 14.09 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: -0.03 (0.15), residues: 3233 helix: 0.71 (0.27), residues: 398 sheet: -0.13 (0.15), residues: 1088 loop : 0.01 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 56 TYR 0.023 0.002 TYR R 49 PHE 0.020 0.002 PHE O 78 TRP 0.018 0.002 TRP S 47 HIS 0.005 0.001 HIS O 95 Details of bonding type rmsd covalent geometry : bond 0.00499 (26890) covalent geometry : angle 0.56790 (36494) SS BOND : bond 0.00461 ( 47) SS BOND : angle 1.20040 ( 94) hydrogen bonds : bond 0.04066 ( 726) hydrogen bonds : angle 5.15665 ( 1842) link_ALPHA1-3 : bond 0.00853 ( 3) link_ALPHA1-3 : angle 1.66806 ( 9) link_BETA1-4 : bond 0.00579 ( 7) link_BETA1-4 : angle 1.55455 ( 21) link_NAG-ASN : bond 0.00487 ( 37) link_NAG-ASN : angle 2.45002 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 392 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8665 (pt0) cc_final: 0.8245 (pt0) REVERT: H 83 ARG cc_start: 0.7477 (ptp-170) cc_final: 0.7259 (ptp-170) REVERT: H 94 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8340 (ttpt) REVERT: A 126 CYS cc_start: 0.7971 (t) cc_final: 0.7619 (t) REVERT: A 232 LYS cc_start: 0.8646 (mttt) cc_final: 0.7427 (tmtt) REVERT: A 347 LYS cc_start: 0.8775 (tttt) cc_final: 0.8394 (ttmt) REVERT: B 574 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7545 (mtpp) REVERT: F 27 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7548 (mm) REVERT: F 42 LYS cc_start: 0.7978 (mttp) cc_final: 0.7080 (mmtt) REVERT: F 81 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7326 (p0) REVERT: F 103 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7474 (mtp85) REVERT: C 116 LEU cc_start: 0.8537 (mt) cc_final: 0.8300 (mm) REVERT: C 136 ASN cc_start: 0.6711 (m-40) cc_final: 0.5937 (p0) REVERT: C 192 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7354 (ttp-110) REVERT: C 232 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7732 (mtpp) REVERT: C 268 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7571 (pt0) REVERT: C 490 LYS cc_start: 0.8870 (pttt) cc_final: 0.8365 (ptmt) REVERT: G 641 ILE cc_start: 0.8921 (mt) cc_final: 0.8679 (mt) REVERT: J 23 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7567 (mmm160) REVERT: J 32 PHE cc_start: 0.8525 (m-80) cc_final: 0.7994 (m-80) REVERT: J 38 ARG cc_start: 0.8660 (ptt180) cc_final: 0.8397 (ptt180) REVERT: M 85 ASP cc_start: 0.7818 (m-30) cc_final: 0.7597 (m-30) REVERT: D 46 LYS cc_start: 0.8719 (mttm) cc_final: 0.8500 (mttm) REVERT: D 99 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8184 (p0) REVERT: D 138 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7292 (pp) REVERT: D 269 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6611 (tp30) REVERT: D 424 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8116 (pt) REVERT: I 535 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8015 (mpt) REVERT: I 588 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7635 (mtm180) REVERT: I 612 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (t) REVERT: I 633 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7819 (mtpt) REVERT: I 657 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: I 661 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8206 (tp) REVERT: K 100 LYS cc_start: 0.8796 (tttp) cc_final: 0.8446 (ttmt) REVERT: N 30 TYR cc_start: 0.9016 (m-80) cc_final: 0.8764 (m-80) REVERT: O 46 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: P 3 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: P 42 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8270 (mmmm) REVERT: Q 73 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (mt) REVERT: S 76 ARG cc_start: 0.8547 (mtm180) cc_final: 0.8302 (mtm180) REVERT: S 105 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: T 24 ARG cc_start: 0.8051 (ttm170) cc_final: 0.7794 (ttm110) REVERT: T 103 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7377 (tmm) REVERT: T 106 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6285 (mt) outliers start: 101 outliers final: 64 residues processed: 447 average time/residue: 0.5610 time to fit residues: 289.5697 Evaluate side-chains 473 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 390 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 639 THR Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 50 TYR Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 24 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN A 103 GLN B 577 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN E 76 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 625 ASN I 656 ASN P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108589 restraints weight = 31624.666| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.90 r_work: 0.3115 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26984 Z= 0.165 Angle : 0.559 14.190 36729 Z= 0.283 Chirality : 0.045 0.399 4164 Planarity : 0.004 0.054 4606 Dihedral : 5.344 51.925 4555 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.10 % Allowed : 14.76 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.02 (0.15), residues: 3233 helix: 0.79 (0.27), residues: 399 sheet: -0.09 (0.15), residues: 1080 loop : 0.03 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 56 TYR 0.020 0.001 TYR Q 50 PHE 0.018 0.002 PHE O 78 TRP 0.017 0.001 TRP S 47 HIS 0.004 0.001 HIS O 95 Details of bonding type rmsd covalent geometry : bond 0.00394 (26890) covalent geometry : angle 0.54069 (36494) SS BOND : bond 0.00405 ( 47) SS BOND : angle 1.09969 ( 94) hydrogen bonds : bond 0.03809 ( 726) hydrogen bonds : angle 5.08445 ( 1842) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.59084 ( 9) link_BETA1-4 : bond 0.00585 ( 7) link_BETA1-4 : angle 1.44044 ( 21) link_NAG-ASN : bond 0.00422 ( 37) link_NAG-ASN : angle 2.35221 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 401 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8644 (pt0) cc_final: 0.8218 (pt0) REVERT: H 83 ARG cc_start: 0.7383 (ptp-170) cc_final: 0.6841 (ptp90) REVERT: H 94 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8368 (ttpt) REVERT: A 126 CYS cc_start: 0.7899 (t) cc_final: 0.7568 (t) REVERT: A 232 LYS cc_start: 0.8621 (mttt) cc_final: 0.7390 (tmtt) REVERT: A 347 LYS cc_start: 0.8755 (tttt) cc_final: 0.8374 (ttmt) REVERT: B 574 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7468 (mtpp) REVERT: E 19 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8473 (tttm) REVERT: F 42 LYS cc_start: 0.7969 (mttp) cc_final: 0.7069 (mmtt) REVERT: F 81 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7287 (p0) REVERT: F 103 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7461 (mtp85) REVERT: C 116 LEU cc_start: 0.8547 (mt) cc_final: 0.8339 (mm) REVERT: C 136 ASN cc_start: 0.6694 (m-40) cc_final: 0.5909 (p0) REVERT: C 192 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7353 (ttp-110) REVERT: C 232 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8117 (mmpt) REVERT: C 424 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (pt) REVERT: C 490 LYS cc_start: 0.8847 (pttt) cc_final: 0.8350 (ptmt) REVERT: G 641 ILE cc_start: 0.8892 (mt) cc_final: 0.8660 (mt) REVERT: J 23 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7614 (mmm160) REVERT: J 32 PHE cc_start: 0.8490 (m-80) cc_final: 0.7965 (m-80) REVERT: J 38 ARG cc_start: 0.8648 (ptt180) cc_final: 0.8383 (ptt180) REVERT: D 46 LYS cc_start: 0.8691 (mttm) cc_final: 0.8473 (mttm) REVERT: D 138 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7278 (pp) REVERT: D 178 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7775 (ttpp) REVERT: D 246 GLN cc_start: 0.7963 (pm20) cc_final: 0.6820 (tp40) REVERT: D 269 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6586 (tp30) REVERT: I 535 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8026 (mpp) REVERT: I 588 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7598 (mtm180) REVERT: I 633 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7791 (mtpt) REVERT: I 640 GLN cc_start: 0.8509 (tp40) cc_final: 0.8150 (tp40) REVERT: I 657 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: I 661 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8109 (tp) REVERT: K 100 LYS cc_start: 0.8763 (tttp) cc_final: 0.8420 (ttmt) REVERT: N 30 TYR cc_start: 0.8998 (m-80) cc_final: 0.8763 (m-80) REVERT: O 46 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: P 3 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: P 42 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8276 (mmmm) REVERT: P 50 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7371 (ttt-90) REVERT: Q 73 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8497 (mt) REVERT: S 76 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8285 (mtm180) REVERT: S 105 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: T 24 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7739 (ttm110) REVERT: T 103 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7352 (tmm) REVERT: T 106 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6258 (mt) outliers start: 88 outliers final: 58 residues processed: 449 average time/residue: 0.5580 time to fit residues: 288.7160 Evaluate side-chains 469 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 391 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 233 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 216 optimal weight: 0.0050 chunk 166 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 27 GLN A 103 GLN A 195 ASN B 577 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 656 ASN K 82AHIS ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110587 restraints weight = 31420.461| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.88 r_work: 0.3142 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26984 Z= 0.125 Angle : 0.532 13.589 36729 Z= 0.269 Chirality : 0.044 0.378 4164 Planarity : 0.004 0.060 4606 Dihedral : 5.170 51.495 4555 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.68 % Allowed : 15.36 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.12 (0.15), residues: 3233 helix: 0.94 (0.27), residues: 397 sheet: -0.02 (0.15), residues: 1073 loop : 0.07 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 56 TYR 0.019 0.001 TYR Q 50 PHE 0.018 0.001 PHE O 78 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS E 82A Details of bonding type rmsd covalent geometry : bond 0.00294 (26890) covalent geometry : angle 0.51354 (36494) SS BOND : bond 0.00330 ( 47) SS BOND : angle 1.03776 ( 94) hydrogen bonds : bond 0.03508 ( 726) hydrogen bonds : angle 4.97463 ( 1842) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.53274 ( 9) link_BETA1-4 : bond 0.00554 ( 7) link_BETA1-4 : angle 1.34374 ( 21) link_NAG-ASN : bond 0.00383 ( 37) link_NAG-ASN : angle 2.31266 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6466 Ramachandran restraints generated. 3233 Oldfield, 0 Emsley, 3233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 401 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8652 (pt0) cc_final: 0.8228 (pt0) REVERT: H 83 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7179 (ptp90) REVERT: H 94 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8451 (ttpt) REVERT: A 126 CYS cc_start: 0.7871 (t) cc_final: 0.7559 (t) REVERT: A 232 LYS cc_start: 0.8636 (mttt) cc_final: 0.7408 (tmtt) REVERT: A 347 LYS cc_start: 0.8746 (tttt) cc_final: 0.8393 (ttmt) REVERT: B 574 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7461 (mtpp) REVERT: F 42 LYS cc_start: 0.7902 (mttp) cc_final: 0.7001 (mmtt) REVERT: F 81 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7357 (p0) REVERT: F 103 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7517 (mtp85) REVERT: C 136 ASN cc_start: 0.6706 (m-40) cc_final: 0.5937 (p0) REVERT: C 192 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7435 (ttp-110) REVERT: C 232 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8137 (mmpt) REVERT: C 424 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8028 (pt) REVERT: C 490 LYS cc_start: 0.8858 (pttt) cc_final: 0.8367 (ptmt) REVERT: G 641 ILE cc_start: 0.8861 (mt) cc_final: 0.8612 (mt) REVERT: J 23 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7621 (mmm160) REVERT: J 38 ARG cc_start: 0.8662 (ptt180) cc_final: 0.8395 (ptt180) REVERT: M 45 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7746 (ttmm) REVERT: D 46 LYS cc_start: 0.8697 (mttm) cc_final: 0.8477 (mttm) REVERT: D 153 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7419 (mm-30) REVERT: D 178 LYS cc_start: 0.8229 (tttm) cc_final: 0.7814 (ttpp) REVERT: D 269 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6547 (tp30) REVERT: D 424 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8094 (pt) REVERT: I 535 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8070 (mpp) REVERT: I 588 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7642 (mtm180) REVERT: I 633 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7814 (mtpt) REVERT: I 640 GLN cc_start: 0.8501 (tp40) cc_final: 0.8136 (tp40) REVERT: I 648 GLU cc_start: 0.8045 (tt0) cc_final: 0.7758 (tm-30) REVERT: I 657 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: I 661 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7987 (tp) REVERT: K 100 LYS cc_start: 0.8820 (tttp) cc_final: 0.8522 (tttt) REVERT: N 30 TYR cc_start: 0.8999 (m-80) cc_final: 0.8708 (m-80) REVERT: O 46 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: P 3 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: P 42 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8310 (mmmm) REVERT: Q 73 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8475 (mt) REVERT: R 94 THR cc_start: 0.8239 (p) cc_final: 0.7857 (p) REVERT: S 76 ARG cc_start: 0.8503 (mtm180) cc_final: 0.8289 (mtm180) REVERT: S 105 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: T 24 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7747 (ttm110) REVERT: T 103 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7379 (tmm) REVERT: T 106 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.6256 (mt) outliers start: 76 outliers final: 52 residues processed: 446 average time/residue: 0.5728 time to fit residues: 295.2005 Evaluate side-chains 460 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 391 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain G residue 538 THR Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 639 THR Chi-restraints excluded: chain I residue 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 105 GLN Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Chi-restraints excluded: chain T residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 78 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 187 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 275 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 650 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN K 82AHIS P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109605 restraints weight = 31334.760| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.94 r_work: 0.3117 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26984 Z= 0.149 Angle : 0.548 13.701 36729 Z= 0.276 Chirality : 0.044 0.388 4164 Planarity : 0.004 0.060 4606 Dihedral : 5.181 55.362 4554 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.75 % Allowed : 15.54 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % 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: 0.11 (0.15), residues: 3233 helix: 0.91 (0.27), residues: 399 sheet: -0.00 (0.15), residues: 1073 loop : 0.05 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 56 TYR 0.020 0.001 TYR Q 50 PHE 0.018 0.002 PHE O 78 TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00356 (26890) covalent geometry : angle 0.53069 (36494) SS BOND : bond 0.00362 ( 47) SS BOND : angle 1.07784 ( 94) hydrogen bonds : bond 0.03619 ( 726) hydrogen bonds : angle 4.97925 ( 1842) link_ALPHA1-3 : bond 0.00793 ( 3) link_ALPHA1-3 : angle 1.52301 ( 9) link_BETA1-4 : bond 0.00535 ( 7) link_BETA1-4 : angle 1.40271 ( 21) link_NAG-ASN : bond 0.00402 ( 37) link_NAG-ASN : angle 2.26836 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8624.08 seconds wall clock time: 147 minutes 43.69 seconds (8863.69 seconds total)