Starting phenix.real_space_refine on Sun Jun 22 15:35:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw4_40797/06_2025/8sw4_40797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw4_40797/06_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_40797/06_2025/8sw4_40797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw4_40797/06_2025/8sw4_40797.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw4_40797/06_2025/8sw4_40797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw4_40797/06_2025/8sw4_40797.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.70, per 1000 atoms: 0.60 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: 6.74 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.06 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: 8.85 Time building geometry restraints manager: 7.66 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 664 or resid 701 thro \ ugh 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.220 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.230 ------------------------------------------------------------------------------- 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 : 2.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.003 TRP O 47 HIS 0.022 0.003 HIS H 35 PHE 0.037 0.003 PHE C 210 TYR 0.045 0.004 TYR Q 50 ARG 0.019 0.002 ARG N 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 37) link_NAG-ASN : angle 3.39598 ( 111) link_BETA1-4 : bond 0.01016 ( 7) link_BETA1-4 : angle 3.69643 ( 21) link_ALPHA1-3 : bond 0.00584 ( 3) link_ALPHA1-3 : angle 0.96961 ( 9) hydrogen bonds : bond 0.12670 ( 726) hydrogen bonds : angle 7.04841 ( 1842) SS BOND : bond 0.07165 ( 47) SS BOND : angle 4.86517 ( 94) covalent geometry : bond 0.00722 (26890) covalent geometry : angle 1.16545 (36494) *********************** 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 : 2.603 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: 0.8192 (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: 0.8327 (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: 0.8479 (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: 1.4375 time to fit residues: 878.3863 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 : 2.739 ------------------------------------------------------------------------------- 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 270 optimal weight: 0.8980 chunk 242 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 0.0370 chunk 129 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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** 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 79 GLN C 114 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 630 GLN J 81 GLN J 82AHIS M 17 GLN M 53 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN I 652 GLN I 656 ASN K 76 ASN N 39 HIS P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 HIS ** 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 = 0.3694 r_free = 0.3694 target = 0.146859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115760 restraints weight = 31148.626| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.3207 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26984 Z= 0.159 Angle : 0.621 16.304 36729 Z= 0.322 Chirality : 0.047 0.547 4164 Planarity : 0.004 0.041 4606 Dihedral : 7.748 77.585 4559 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.43 % Allowed : 10.96 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3233 helix: 0.61 (0.27), residues: 408 sheet: 0.46 (0.15), residues: 1095 loop : 0.43 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 103 HIS 0.005 0.001 HIS Q 74 PHE 0.020 0.002 PHE O 78 TYR 0.021 0.001 TYR Q 50 ARG 0.006 0.001 ARG C 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 37) link_NAG-ASN : angle 2.88313 ( 111) link_BETA1-4 : bond 0.00810 ( 7) link_BETA1-4 : angle 2.51940 ( 21) link_ALPHA1-3 : bond 0.00874 ( 3) link_ALPHA1-3 : angle 2.13937 ( 9) hydrogen bonds : bond 0.04751 ( 726) hydrogen bonds : angle 5.75294 ( 1842) SS BOND : bond 0.00370 ( 47) SS BOND : angle 1.14074 ( 94) covalent geometry : bond 0.00363 (26890) covalent geometry : angle 0.59533 (36494) *********************** 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 526 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 457 time to evaluate : 2.871 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8558 (pt0) cc_final: 0.8142 (pt0) REVERT: H 46 GLU cc_start: 0.8604 (tt0) cc_final: 0.8395 (tt0) REVERT: H 83 ARG cc_start: 0.7397 (ptp-170) cc_final: 0.7059 (ptp-170) REVERT: H 94 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8153 (ttpt) REVERT: A 141 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6416 (p0) REVERT: A 232 LYS cc_start: 0.8368 (mttt) cc_final: 0.7014 (tmtt) REVERT: A 278 ARG cc_start: 0.8467 (mmp80) cc_final: 0.8239 (mmp80) REVERT: A 347 LYS cc_start: 0.8615 (tttt) cc_final: 0.8252 (ttmt) REVERT: E 19 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8197 (ttmt) REVERT: F 42 LYS cc_start: 0.7476 (mttp) cc_final: 0.6484 (mmtt) REVERT: F 103 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7357 (mtp85) REVERT: C 136 ASN cc_start: 0.6552 (m-40) cc_final: 0.5643 (p0) REVERT: C 161 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7318 (ttp) REVERT: G 641 ILE cc_start: 0.8768 (mt) cc_final: 0.8512 (mt) REVERT: D 46 LYS cc_start: 0.8683 (mttm) cc_final: 0.8344 (mttm) REVERT: D 153 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7329 (mm-30) REVERT: D 231 LYS cc_start: 0.8200 (mttt) cc_final: 0.7991 (mppt) REVERT: I 632 ASP cc_start: 0.8282 (t0) cc_final: 0.7785 (t0) REVERT: I 633 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7632 (mtpt) REVERT: K 100 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8409 (tttp) REVERT: N 30 TYR cc_start: 0.8865 (m-80) cc_final: 0.8565 (m-80) REVERT: N 85 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: O 11 ARG cc_start: 0.6122 (mtp85) cc_final: 0.5787 (mmt-90) REVERT: P 3 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: P 106 ILE cc_start: 0.5226 (OUTLIER) cc_final: 0.4829 (pp) REVERT: Q 100 TYR cc_start: 0.8384 (m-80) cc_final: 0.8053 (m-80) REVERT: S 27 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8025 (m-30) outliers start: 69 outliers final: 31 residues processed: 491 average time/residue: 1.3707 time to fit residues: 781.8333 Evaluate side-chains 447 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 410 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 612 SER 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 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 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 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 R residue 58 VAL Chi-restraints excluded: chain S residue 27 ASP 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 42 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 27 GLN L 92 ASN A 33 ASN A 283 ASN A 315 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN F 38 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN J 82AHIS M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN K 81 GLN K 82AHIS P 28 ASN Q 60 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN T 31 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113094 restraints weight = 31280.173| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.87 r_work: 0.3160 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26984 Z= 0.156 Angle : 0.573 15.044 36729 Z= 0.294 Chirality : 0.046 0.426 4164 Planarity : 0.004 0.041 4606 Dihedral : 6.506 59.950 4559 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.92 % Allowed : 11.56 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3233 helix: 0.66 (0.27), residues: 414 sheet: 0.31 (0.15), residues: 1096 loop : 0.35 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 103 HIS 0.005 0.001 HIS Q 74 PHE 0.020 0.002 PHE O 78 TYR 0.021 0.001 TYR Q 50 ARG 0.009 0.001 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 37) link_NAG-ASN : angle 2.58656 ( 111) link_BETA1-4 : bond 0.00671 ( 7) link_BETA1-4 : angle 1.89789 ( 21) link_ALPHA1-3 : bond 0.00983 ( 3) link_ALPHA1-3 : angle 1.64844 ( 9) hydrogen bonds : bond 0.04120 ( 726) hydrogen bonds : angle 5.29000 ( 1842) SS BOND : bond 0.00381 ( 47) SS BOND : angle 1.07924 ( 94) covalent geometry : bond 0.00364 (26890) covalent geometry : angle 0.55145 (36494) *********************** 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 519 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 436 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8628 (pt0) cc_final: 0.8209 (pt0) REVERT: H 74 SER cc_start: 0.8459 (p) cc_final: 0.8038 (m) REVERT: H 83 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.7027 (ptp-170) REVERT: H 94 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8397 (ttpt) REVERT: A 126 CYS cc_start: 0.7832 (t) cc_final: 0.7485 (t) REVERT: A 141 ASP cc_start: 0.6769 (OUTLIER) cc_final: 0.6532 (p0) REVERT: A 192 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7829 (ptm-80) REVERT: A 232 LYS cc_start: 0.8426 (mttt) cc_final: 0.7094 (tmtt) REVERT: A 347 LYS cc_start: 0.8636 (tttt) cc_final: 0.8303 (ttmt) REVERT: B 647 GLU cc_start: 0.7395 (tt0) cc_final: 0.7114 (tt0) REVERT: E 19 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8216 (ttmt) REVERT: E 82 MET cc_start: 0.8713 (mtm) cc_final: 0.8201 (mtp) REVERT: F 42 LYS cc_start: 0.7739 (mttp) cc_final: 0.6736 (mmtt) REVERT: C 136 ASN cc_start: 0.6610 (m-40) cc_final: 0.5815 (p0) REVERT: C 232 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7885 (mtpp) REVERT: G 641 ILE cc_start: 0.8820 (mt) cc_final: 0.8568 (mt) REVERT: J 23 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7649 (mmm160) REVERT: D 46 LYS cc_start: 0.8754 (mttm) cc_final: 0.8464 (mttm) REVERT: D 231 LYS cc_start: 0.8303 (mttt) cc_final: 0.8016 (mppt) REVERT: I 633 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7642 (mtpt) REVERT: N 30 TYR cc_start: 0.8914 (m-80) cc_final: 0.8627 (m-80) REVERT: O 11 ARG cc_start: 0.6246 (mtp85) cc_final: 0.5897 (mmt-90) REVERT: T 17 ASP cc_start: 0.6205 (m-30) cc_final: 0.5560 (m-30) outliers start: 83 outliers final: 43 residues processed: 478 average time/residue: 1.3262 time to fit residues: 737.9363 Evaluate side-chains 449 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 2.688 ------------------------------------------------------------------------------- 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 65 SER 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 465 THR 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 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 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 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 198 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 340 GLU 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 661 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 LEU 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 10 SER Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 110 THR 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 108 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 163 optimal weight: 0.0670 chunk 267 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 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** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 630 GLN I 656 ASN K 81 GLN N 31 ASN P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 HIS 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 = 0.3620 r_free = 0.3620 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108970 restraints weight = 31683.635| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.89 r_work: 0.3118 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2187 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= 0.207 Angle : 0.607 14.912 36729 Z= 0.308 Chirality : 0.047 0.435 4164 Planarity : 0.004 0.069 4606 Dihedral : 5.844 52.627 4557 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.45 % Allowed : 12.26 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3233 helix: 0.67 (0.27), residues: 406 sheet: 0.13 (0.15), residues: 1083 loop : 0.19 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 103 HIS 0.005 0.001 HIS O 74 PHE 0.021 0.002 PHE O 78 TYR 0.024 0.002 TYR R 49 ARG 0.011 0.001 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 37) link_NAG-ASN : angle 2.50793 ( 111) link_BETA1-4 : bond 0.00633 ( 7) link_BETA1-4 : angle 1.84047 ( 21) link_ALPHA1-3 : bond 0.00940 ( 3) link_ALPHA1-3 : angle 1.76872 ( 9) hydrogen bonds : bond 0.04245 ( 726) hydrogen bonds : angle 5.21240 ( 1842) SS BOND : bond 0.00478 ( 47) SS BOND : angle 1.34534 ( 94) covalent geometry : bond 0.00497 (26890) covalent geometry : angle 0.58680 (36494) *********************** 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 520 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 422 time to evaluate : 2.753 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8716 (pt0) cc_final: 0.8331 (pt0) REVERT: H 83 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.6886 (ptp90) REVERT: H 94 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8539 (ttpt) REVERT: A 126 CYS cc_start: 0.8000 (t) cc_final: 0.7652 (t) REVERT: A 141 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6494 (p0) REVERT: A 232 LYS cc_start: 0.8647 (mttt) cc_final: 0.7430 (tmtt) REVERT: A 347 LYS cc_start: 0.8724 (tttt) cc_final: 0.8430 (ttmt) REVERT: F 42 LYS cc_start: 0.7901 (mttp) cc_final: 0.6959 (mmpt) REVERT: C 136 ASN cc_start: 0.6754 (m-40) cc_final: 0.5859 (p0) REVERT: C 232 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7999 (mtpp) REVERT: G 641 ILE cc_start: 0.8921 (mt) cc_final: 0.8677 (mt) REVERT: J 23 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7697 (mmm160) REVERT: D 46 LYS cc_start: 0.8725 (mttm) cc_final: 0.8465 (mttm) REVERT: D 99 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8271 (p0) REVERT: D 138 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7158 (pp) REVERT: I 588 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7730 (mtm-85) REVERT: I 633 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7721 (mtpt) REVERT: I 657 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: I 661 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (tp) REVERT: K 100 LYS cc_start: 0.8868 (tttp) cc_final: 0.8367 (tttt) REVERT: N 30 TYR cc_start: 0.9006 (m-80) cc_final: 0.8778 (m-80) REVERT: O 11 ARG cc_start: 0.6035 (mtp85) cc_final: 0.5706 (mmt-90) REVERT: P 3 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8058 (mt0) outliers start: 98 outliers final: 43 residues processed: 475 average time/residue: 1.4167 time to fit residues: 783.0702 Evaluate side-chains 452 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 3.364 ------------------------------------------------------------------------------- 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 24 ARG Chi-restraints excluded: chain L residue 65 SER 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 465 THR 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 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 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 426 MET Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 636 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 22 CYS Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 63 SER 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 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 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 P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 248 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 27 GLN B 607 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3634 r_free = 0.3634 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110047 restraints weight = 31472.951| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.91 r_work: 0.3129 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26984 Z= 0.153 Angle : 0.552 14.438 36729 Z= 0.280 Chirality : 0.045 0.406 4164 Planarity : 0.004 0.059 4606 Dihedral : 5.461 51.846 4557 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.82 % Allowed : 13.39 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3233 helix: 0.78 (0.27), residues: 401 sheet: 0.11 (0.15), residues: 1093 loop : 0.19 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.007 0.001 HIS H 35 PHE 0.018 0.002 PHE O 78 TYR 0.019 0.001 TYR Q 50 ARG 0.010 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 37) link_NAG-ASN : angle 2.37303 ( 111) link_BETA1-4 : bond 0.00627 ( 7) link_BETA1-4 : angle 1.56027 ( 21) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.67552 ( 9) hydrogen bonds : bond 0.03827 ( 726) hydrogen bonds : angle 5.08692 ( 1842) SS BOND : bond 0.00405 ( 47) SS BOND : angle 1.17002 ( 94) covalent geometry : bond 0.00363 (26890) covalent geometry : angle 0.53297 (36494) *********************** 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 493 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 413 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8702 (pt0) cc_final: 0.8305 (pt0) REVERT: H 83 ARG cc_start: 0.7362 (ptp-170) cc_final: 0.6782 (ptp90) REVERT: H 94 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8289 (ttpt) REVERT: A 52 LEU cc_start: 0.8921 (mt) cc_final: 0.8680 (mp) REVERT: A 126 CYS cc_start: 0.7810 (t) cc_final: 0.7469 (t) REVERT: A 141 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6474 (p0) REVERT: A 232 LYS cc_start: 0.8639 (mttt) cc_final: 0.7353 (tmtt) REVERT: A 347 LYS cc_start: 0.8698 (tttt) cc_final: 0.8355 (ttmt) REVERT: F 42 LYS cc_start: 0.7862 (mttp) cc_final: 0.6920 (mmtt) REVERT: F 45 LYS cc_start: 0.8521 (tttt) cc_final: 0.8306 (tttt) REVERT: C 136 ASN cc_start: 0.6753 (m-40) cc_final: 0.5838 (p0) REVERT: C 232 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7969 (mtpp) REVERT: G 641 ILE cc_start: 0.8858 (mt) cc_final: 0.8610 (mt) REVERT: J 23 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7609 (mmm160) REVERT: M 45 LYS cc_start: 0.8343 (ttpp) cc_final: 0.7834 (ttmm) REVERT: M 53 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7479 (mm110) REVERT: M 85 ASP cc_start: 0.7662 (m-30) cc_final: 0.7447 (m-30) REVERT: D 46 LYS cc_start: 0.8658 (mttm) cc_final: 0.8430 (mttm) REVERT: D 138 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7119 (pp) REVERT: D 178 LYS cc_start: 0.8242 (tttm) cc_final: 0.7617 (tttm) REVERT: I 535 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7978 (mpp) REVERT: I 588 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7633 (mtm-85) REVERT: I 633 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7664 (mtpt) REVERT: I 657 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: I 661 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8131 (tp) REVERT: K 100 LYS cc_start: 0.8766 (tttp) cc_final: 0.8494 (ttmt) REVERT: N 30 TYR cc_start: 0.8980 (m-80) cc_final: 0.8685 (m-80) REVERT: O 46 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: P 3 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: P 51 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (t) REVERT: T 17 ASP cc_start: 0.6391 (m-30) cc_final: 0.5733 (m-30) REVERT: T 103 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7202 (tmm) outliers start: 80 outliers final: 47 residues processed: 459 average time/residue: 1.4063 time to fit residues: 750.8026 Evaluate side-chains 457 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 400 time to evaluate : 2.642 ------------------------------------------------------------------------------- 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 H residue 107 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain A residue 141 ASP 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 595 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 87 THR 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 97 ILE 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 G residue 599 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 664 ASP Chi-restraints excluded: chain J residue 5 VAL 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 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 535 MET 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 83 THR Chi-restraints excluded: chain P residue 3 GLN Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 124 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 27 GLN A 103 GLN B 577 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 656 ASN 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 = 0.3624 r_free = 0.3624 target = 0.140978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109394 restraints weight = 31496.729| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.92 r_work: 0.3116 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26984 Z= 0.173 Angle : 0.563 14.374 36729 Z= 0.284 Chirality : 0.045 0.404 4164 Planarity : 0.004 0.053 4606 Dihedral : 5.362 52.185 4557 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 13.07 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3233 helix: 0.77 (0.27), residues: 401 sheet: 0.04 (0.15), residues: 1088 loop : 0.14 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.007 0.001 HIS H 35 PHE 0.019 0.002 PHE O 78 TYR 0.020 0.001 TYR R 49 ARG 0.010 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 37) link_NAG-ASN : angle 2.38932 ( 111) link_BETA1-4 : bond 0.00622 ( 7) link_BETA1-4 : angle 1.57968 ( 21) link_ALPHA1-3 : bond 0.00938 ( 3) link_ALPHA1-3 : angle 1.66054 ( 9) hydrogen bonds : bond 0.03867 ( 726) hydrogen bonds : angle 5.07208 ( 1842) SS BOND : bond 0.00413 ( 47) SS BOND : angle 1.13079 ( 94) covalent geometry : bond 0.00415 (26890) covalent geometry : angle 0.54406 (36494) *********************** 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 496 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 405 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8672 (pt0) cc_final: 0.8278 (pt0) REVERT: H 94 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8338 (ttpt) REVERT: A 52 LEU cc_start: 0.8965 (mt) cc_final: 0.8738 (mp) REVERT: A 126 CYS cc_start: 0.7979 (t) cc_final: 0.7631 (t) REVERT: A 141 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6511 (p0) REVERT: A 232 LYS cc_start: 0.8650 (mttt) cc_final: 0.7362 (tmtt) REVERT: A 347 LYS cc_start: 0.8709 (tttt) cc_final: 0.8351 (ttmt) REVERT: F 27 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7554 (mm) REVERT: F 69 ASN cc_start: 0.8008 (m-40) cc_final: 0.7788 (m-40) REVERT: F 103 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7371 (mtp85) REVERT: C 136 ASN cc_start: 0.6622 (m-40) cc_final: 0.5736 (p0) REVERT: C 232 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8199 (mmpt) REVERT: C 490 LYS cc_start: 0.8878 (pttt) cc_final: 0.8347 (ptmt) REVERT: G 641 ILE cc_start: 0.8858 (mt) cc_final: 0.8624 (mt) REVERT: J 23 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7597 (mmm160) REVERT: M 85 ASP cc_start: 0.7618 (m-30) cc_final: 0.7390 (m-30) REVERT: D 46 LYS cc_start: 0.8667 (mttm) cc_final: 0.8430 (mttm) REVERT: D 99 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 138 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7150 (pp) REVERT: D 424 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (pt) REVERT: I 535 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7984 (mpp) REVERT: I 588 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7671 (mtm-85) REVERT: I 633 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7697 (mtpt) REVERT: I 657 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: I 661 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8141 (tp) REVERT: K 82 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: K 100 LYS cc_start: 0.8817 (tttp) cc_final: 0.8398 (ttmt) REVERT: N 30 TYR cc_start: 0.8982 (m-80) cc_final: 0.8697 (m-80) REVERT: O 46 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: P 3 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: P 51 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7752 (t) REVERT: T 103 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7278 (tmm) outliers start: 91 outliers final: 55 residues processed: 454 average time/residue: 1.4484 time to fit residues: 765.7554 Evaluate side-chains 470 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 400 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 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 92 GLU Chi-restraints excluded: chain A residue 141 ASP 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 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 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 636 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 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 535 MET 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 657 GLU Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain K residue 82 MET 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 51 THR Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 102 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 27 GLN A 99 ASN 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** J 13 GLN M 53 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN I 656 ASN K 82AHIS 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107055 restraints weight = 31799.581| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.95 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26984 Z= 0.222 Angle : 0.607 14.740 36729 Z= 0.306 Chirality : 0.047 0.415 4164 Planarity : 0.004 0.053 4606 Dihedral : 5.558 52.898 4557 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.52 % Allowed : 13.32 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3233 helix: 0.68 (0.27), residues: 399 sheet: -0.10 (0.15), residues: 1091 loop : 0.04 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.008 0.001 HIS H 35 PHE 0.022 0.002 PHE O 78 TYR 0.026 0.002 TYR R 49 ARG 0.012 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 37) link_NAG-ASN : angle 2.49812 ( 111) link_BETA1-4 : bond 0.00580 ( 7) link_BETA1-4 : angle 1.63939 ( 21) link_ALPHA1-3 : bond 0.00857 ( 3) link_ALPHA1-3 : angle 1.69704 ( 9) hydrogen bonds : bond 0.04168 ( 726) hydrogen bonds : angle 5.17004 ( 1842) SS BOND : bond 0.00492 ( 47) SS BOND : angle 1.32782 ( 94) covalent geometry : bond 0.00533 (26890) covalent geometry : angle 0.58714 (36494) *********************** 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 507 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 407 time to evaluate : 2.582 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8670 (pt0) cc_final: 0.8278 (pt0) REVERT: H 83 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.6840 (ptp90) REVERT: H 94 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8325 (ttpt) REVERT: A 52 LEU cc_start: 0.9015 (mt) cc_final: 0.8742 (mp) REVERT: A 103 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: A 126 CYS cc_start: 0.7934 (t) cc_final: 0.7585 (t) REVERT: A 232 LYS cc_start: 0.8659 (mttt) cc_final: 0.7425 (tmtt) REVERT: A 347 LYS cc_start: 0.8765 (tttt) cc_final: 0.8395 (ttmt) REVERT: B 574 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7451 (mtpp) REVERT: B 660 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8461 (mt) REVERT: F 27 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7575 (mm) REVERT: F 42 LYS cc_start: 0.7903 (mttp) cc_final: 0.6975 (mmtt) REVERT: F 69 ASN cc_start: 0.8128 (m-40) cc_final: 0.7900 (m-40) REVERT: F 103 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7380 (mtp85) REVERT: C 136 ASN cc_start: 0.6694 (m-40) cc_final: 0.5779 (p0) REVERT: C 232 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7942 (mtpp) REVERT: G 636 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8158 (p) REVERT: G 641 ILE cc_start: 0.8909 (mt) cc_final: 0.8685 (mt) REVERT: J 23 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7586 (mmm160) REVERT: J 32 PHE cc_start: 0.8460 (m-80) cc_final: 0.7920 (m-80) REVERT: M 53 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7606 (mm110) REVERT: M 85 ASP cc_start: 0.7750 (m-30) cc_final: 0.7509 (m-30) REVERT: D 46 LYS cc_start: 0.8706 (mttm) cc_final: 0.8450 (mttm) REVERT: D 99 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8261 (p0) REVERT: D 138 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7250 (pp) REVERT: D 178 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7788 (ttpp) REVERT: D 269 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: D 424 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8134 (pt) REVERT: D 475 MET cc_start: 0.8889 (mmp) cc_final: 0.8629 (mmp) REVERT: I 535 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8047 (mpp) REVERT: I 588 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7631 (mtm180) REVERT: I 612 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8443 (t) REVERT: I 633 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7740 (mtpt) REVERT: I 657 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: I 661 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8344 (tp) REVERT: K 100 LYS cc_start: 0.8788 (tttp) cc_final: 0.8374 (ttmt) REVERT: N 30 TYR cc_start: 0.8997 (m-80) cc_final: 0.8741 (m-80) REVERT: O 46 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: P 3 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: P 51 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7623 (t) REVERT: T 17 ASP cc_start: 0.6430 (m-30) cc_final: 0.5792 (m-30) REVERT: T 103 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7276 (tmm) outliers start: 100 outliers final: 63 residues processed: 455 average time/residue: 1.3450 time to fit residues: 711.8636 Evaluate side-chains 482 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 399 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET 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 L residue 107 LYS Chi-restraints excluded: chain A residue 92 GLU 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 B residue 660 LEU 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 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 636 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 M residue 63 SER 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 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 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 33 LEU Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 80 SER Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain S residue 31 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 27 GLN B 577 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** M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN I 625 ASN I 656 ASN O 5 GLN P 28 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108716 restraints weight = 31609.870| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.85 r_work: 0.3124 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26984 Z= 0.164 Angle : 0.564 14.415 36729 Z= 0.285 Chirality : 0.045 0.405 4164 Planarity : 0.004 0.056 4606 Dihedral : 5.361 52.177 4555 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.17 % Allowed : 13.92 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3233 helix: 0.77 (0.27), residues: 399 sheet: -0.10 (0.15), residues: 1084 loop : 0.04 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.006 0.001 HIS H 35 PHE 0.018 0.002 PHE O 78 TYR 0.019 0.001 TYR R 49 ARG 0.013 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 37) link_NAG-ASN : angle 2.42887 ( 111) link_BETA1-4 : bond 0.00567 ( 7) link_BETA1-4 : angle 1.48178 ( 21) link_ALPHA1-3 : bond 0.00894 ( 3) link_ALPHA1-3 : angle 1.63867 ( 9) hydrogen bonds : bond 0.03866 ( 726) hydrogen bonds : angle 5.08708 ( 1842) SS BOND : bond 0.00415 ( 47) SS BOND : angle 1.16865 ( 94) covalent geometry : bond 0.00392 (26890) covalent geometry : angle 0.54433 (36494) *********************** 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 494 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 404 time to evaluate : 3.266 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8634 (pt0) cc_final: 0.8232 (pt0) REVERT: H 83 ARG cc_start: 0.7338 (ptp-170) cc_final: 0.6927 (ptp90) REVERT: H 94 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8342 (ttpt) REVERT: L 11 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6197 (tp) REVERT: A 52 LEU cc_start: 0.9009 (mt) cc_final: 0.8723 (mp) REVERT: A 126 CYS cc_start: 0.7949 (t) cc_final: 0.7604 (t) REVERT: A 232 LYS cc_start: 0.8657 (mttt) cc_final: 0.7427 (tmtt) REVERT: A 347 LYS cc_start: 0.8742 (tttt) cc_final: 0.8365 (ttmt) REVERT: F 27 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7565 (mm) REVERT: F 42 LYS cc_start: 0.7874 (mttp) cc_final: 0.6978 (mmtt) REVERT: F 45 LYS cc_start: 0.8593 (tttt) cc_final: 0.8022 (ptmm) REVERT: F 69 ASN cc_start: 0.8113 (m-40) cc_final: 0.7900 (m-40) REVERT: F 103 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7399 (mtp85) REVERT: C 136 ASN cc_start: 0.6698 (m-40) cc_final: 0.5781 (p0) REVERT: C 232 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (mmpt) REVERT: C 490 LYS cc_start: 0.8847 (pttt) cc_final: 0.8353 (ptmt) REVERT: G 636 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8135 (p) REVERT: G 641 ILE cc_start: 0.8892 (mt) cc_final: 0.8661 (mt) REVERT: J 23 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7575 (mmm160) REVERT: J 32 PHE cc_start: 0.8414 (m-80) cc_final: 0.7899 (m-80) REVERT: M 85 ASP cc_start: 0.7726 (m-30) cc_final: 0.7493 (m-30) REVERT: D 46 LYS cc_start: 0.8696 (mttm) cc_final: 0.8458 (mttm) REVERT: D 99 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8236 (p0) REVERT: D 138 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7282 (pp) REVERT: D 178 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7798 (ttpp) REVERT: D 424 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8085 (pt) REVERT: I 535 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8000 (mpp) REVERT: I 588 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7595 (mtm180) REVERT: I 633 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7729 (mtpt) REVERT: I 657 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: I 661 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8139 (tp) REVERT: K 82 MET cc_start: 0.8268 (mtm) cc_final: 0.7981 (mtt) REVERT: K 100 LYS cc_start: 0.8734 (tttp) cc_final: 0.8321 (ttmt) REVERT: N 30 TYR cc_start: 0.8995 (m-80) cc_final: 0.8743 (m-80) REVERT: O 46 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: P 3 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: T 17 ASP cc_start: 0.6312 (m-30) cc_final: 0.5730 (m-30) REVERT: T 103 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7298 (tmm) outliers start: 90 outliers final: 56 residues processed: 454 average time/residue: 1.3808 time to fit residues: 729.0056 Evaluate side-chains 464 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 393 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 11 LEU 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 L residue 107 LYS Chi-restraints excluded: chain A residue 92 GLU 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 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 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 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 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 636 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 M residue 63 SER Chi-restraints excluded: chain D residue 99 ASN 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 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 110 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.5980 chunk 292 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 221 optimal weight: 0.0060 chunk 137 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 27 GLN B 650 GLN ** 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** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110654 restraints weight = 31527.519| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.92 r_work: 0.3154 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26984 Z= 0.120 Angle : 0.523 13.606 36729 Z= 0.266 Chirality : 0.043 0.375 4164 Planarity : 0.004 0.054 4606 Dihedral : 5.062 51.437 4555 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.47 % Allowed : 14.90 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3233 helix: 0.91 (0.27), residues: 399 sheet: -0.02 (0.15), residues: 1091 loop : 0.10 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.001 PHE O 78 TYR 0.018 0.001 TYR Q 50 ARG 0.014 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 37) link_NAG-ASN : angle 2.25390 ( 111) link_BETA1-4 : bond 0.00584 ( 7) link_BETA1-4 : angle 1.33452 ( 21) link_ALPHA1-3 : bond 0.00911 ( 3) link_ALPHA1-3 : angle 1.55158 ( 9) hydrogen bonds : bond 0.03469 ( 726) hydrogen bonds : angle 4.95853 ( 1842) SS BOND : bond 0.00334 ( 47) SS BOND : angle 1.01527 ( 94) covalent geometry : bond 0.00280 (26890) covalent geometry : angle 0.50566 (36494) *********************** 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 469 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 399 time to evaluate : 2.833 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8633 (pt0) cc_final: 0.8239 (pt0) REVERT: H 83 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6871 (ptp90) REVERT: H 94 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8282 (ttpt) REVERT: A 52 LEU cc_start: 0.9002 (mt) cc_final: 0.8764 (mp) REVERT: A 103 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7237 (mt0) REVERT: A 126 CYS cc_start: 0.7824 (t) cc_final: 0.7489 (t) REVERT: A 232 LYS cc_start: 0.8647 (mttt) cc_final: 0.7406 (tmtt) REVERT: A 347 LYS cc_start: 0.8718 (tttt) cc_final: 0.8366 (ttmt) REVERT: F 42 LYS cc_start: 0.7853 (mttp) cc_final: 0.6976 (mmtt) REVERT: F 45 LYS cc_start: 0.8422 (tttt) cc_final: 0.8036 (ptmm) REVERT: F 103 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7425 (mtp85) REVERT: C 136 ASN cc_start: 0.6668 (m-40) cc_final: 0.5914 (p0) REVERT: C 232 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8063 (mmpt) REVERT: C 446 VAL cc_start: 0.8578 (t) cc_final: 0.8171 (p) REVERT: C 490 LYS cc_start: 0.8841 (pttt) cc_final: 0.8346 (ptmt) REVERT: G 636 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8123 (p) REVERT: G 641 ILE cc_start: 0.8849 (mt) cc_final: 0.8609 (mt) REVERT: J 23 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7576 (mmm160) REVERT: M 85 ASP cc_start: 0.7650 (m-30) cc_final: 0.7443 (m-30) REVERT: D 46 LYS cc_start: 0.8679 (mttm) cc_final: 0.8416 (mttm) REVERT: D 178 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7785 (ttpp) REVERT: D 424 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8092 (pt) REVERT: I 535 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8068 (mpp) REVERT: I 588 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7603 (mtm180) REVERT: I 633 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7764 (mtpt) REVERT: I 657 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: I 661 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7985 (tp) REVERT: N 30 TYR cc_start: 0.8976 (m-80) cc_final: 0.8748 (m-80) REVERT: O 46 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: P 3 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8180 (mt0) REVERT: Q 73 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8486 (mt) REVERT: R 94 THR cc_start: 0.8234 (p) cc_final: 0.7843 (p) REVERT: T 17 ASP cc_start: 0.6322 (m-30) cc_final: 0.5763 (m-30) REVERT: T 103 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7338 (tmm) outliers start: 70 outliers final: 47 residues processed: 434 average time/residue: 1.3810 time to fit residues: 696.3996 Evaluate side-chains 451 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 390 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 83 ARG 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 A residue 92 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR 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 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 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 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 636 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 M residue 63 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain I residue 535 MET Chi-restraints excluded: chain I residue 599 SER Chi-restraints excluded: chain I residue 612 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 33 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 103 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 66 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** B 577 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 653 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109863 restraints weight = 31493.689| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.91 r_work: 0.3138 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2772 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= 0.152 Angle : 0.547 13.793 36729 Z= 0.277 Chirality : 0.044 0.389 4164 Planarity : 0.004 0.058 4606 Dihedral : 5.103 52.062 4555 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.33 % Allowed : 15.05 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3233 helix: 0.90 (0.27), residues: 399 sheet: -0.01 (0.15), residues: 1092 loop : 0.06 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.006 0.001 HIS H 35 PHE 0.018 0.002 PHE O 78 TYR 0.019 0.001 TYR Q 50 ARG 0.015 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 37) link_NAG-ASN : angle 2.32709 ( 111) link_BETA1-4 : bond 0.00551 ( 7) link_BETA1-4 : angle 1.41445 ( 21) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 1.54129 ( 9) hydrogen bonds : bond 0.03638 ( 726) hydrogen bonds : angle 4.95591 ( 1842) SS BOND : bond 0.00367 ( 47) SS BOND : angle 1.10027 ( 94) covalent geometry : bond 0.00362 (26890) covalent geometry : angle 0.52887 (36494) ********************** 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 461 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 395 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8624 (pt0) cc_final: 0.8231 (pt0) REVERT: H 83 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6899 (ptp90) REVERT: H 94 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8355 (ttpt) REVERT: A 126 CYS cc_start: 0.7868 (t) cc_final: 0.7547 (t) REVERT: A 232 LYS cc_start: 0.8638 (mttt) cc_final: 0.7409 (tmtt) REVERT: A 347 LYS cc_start: 0.8766 (tttt) cc_final: 0.8428 (ttmt) REVERT: F 42 LYS cc_start: 0.7860 (mttp) cc_final: 0.6987 (mmtt) REVERT: F 103 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7472 (mtp85) REVERT: C 136 ASN cc_start: 0.6695 (m-40) cc_final: 0.5804 (p0) REVERT: C 232 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8090 (mmpt) REVERT: G 636 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8143 (p) REVERT: G 641 ILE cc_start: 0.8885 (mt) cc_final: 0.8643 (mt) REVERT: M 45 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7523 (tttm) REVERT: M 85 ASP cc_start: 0.7703 (m-30) cc_final: 0.7491 (m-30) REVERT: D 178 LYS cc_start: 0.8247 (tttm) cc_final: 0.7828 (ttpp) REVERT: D 246 GLN cc_start: 0.7938 (pm20) cc_final: 0.6775 (tp40) REVERT: D 424 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8144 (pt) REVERT: I 535 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: I 588 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7652 (mtm180) REVERT: I 633 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7738 (mtpt) REVERT: I 640 GLN cc_start: 0.8516 (tp40) cc_final: 0.8157 (tp40) REVERT: I 657 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: I 661 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8094 (tp) REVERT: K 100 LYS cc_start: 0.8805 (tttp) cc_final: 0.8533 (tttt) REVERT: N 30 TYR cc_start: 0.8992 (m-80) cc_final: 0.8675 (m-80) REVERT: O 46 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: P 3 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: P 50 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7731 (ttt180) REVERT: Q 73 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8482 (mt) REVERT: S 107 ILE cc_start: 0.8325 (mm) cc_final: 0.7915 (tt) REVERT: T 17 ASP cc_start: 0.6328 (m-30) cc_final: 0.5786 (m-30) outliers start: 66 outliers final: 48 residues processed: 427 average time/residue: 1.3640 time to fit residues: 673.3020 Evaluate side-chains 446 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 388 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 83 ARG 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 A residue 92 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 465 THR 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 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 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 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 636 SER Chi-restraints excluded: chain G residue 639 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 664 ASP 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 25 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 132 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 599 SER Chi-restraints excluded: chain I residue 612 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 110 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 49 optimal weight: 0.0770 chunk 227 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 224 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- 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 6 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 GLN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 GLN M 69 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108109 restraints weight = 31699.813| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.88 r_work: 0.3107 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2820 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= 0.212 Angle : 0.586 14.194 36729 Z= 0.296 Chirality : 0.046 0.410 4164 Planarity : 0.004 0.062 4606 Dihedral : 5.275 52.561 4555 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.57 % Allowed : 15.12 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3233 helix: 0.77 (0.27), residues: 399 sheet: -0.08 (0.15), residues: 1091 loop : 0.01 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.007 0.001 HIS H 35 PHE 0.021 0.002 PHE O 78 TYR 0.024 0.002 TYR R 49 ARG 0.014 0.001 ARG P 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 37) link_NAG-ASN : angle 2.36530 ( 111) link_BETA1-4 : bond 0.00557 ( 7) link_BETA1-4 : angle 1.51417 ( 21) link_ALPHA1-3 : bond 0.00734 ( 3) link_ALPHA1-3 : angle 1.56146 ( 9) hydrogen bonds : bond 0.03934 ( 726) hydrogen bonds : angle 5.04620 ( 1842) SS BOND : bond 0.00444 ( 47) SS BOND : angle 1.19546 ( 94) covalent geometry : bond 0.00512 (26890) covalent geometry : angle 0.56788 (36494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20605.76 seconds wall clock time: 353 minutes 44.48 seconds (21224.48 seconds total)