Starting phenix.real_space_refine on Mon Aug 25 01:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4l_41035/08_2025/8t4l_41035.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 144 5.16 5 C 15303 2.51 5 N 4107 2.21 5 O 4821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24375 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "O" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Q" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3437 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 21, 'TRANS': 411} Chain breaks: 4 Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "P" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 787 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "S" 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.82, per 1000 atoms: 0.24 Number of scatterers: 24375 At special positions: 0 Unit cell: (154.512, 157.644, 170.172, 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 144 16.00 O 4821 8.00 N 4107 7.00 C 15303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 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 BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 241 " " NAG B 701 " - " ASN B 611 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 386 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 289 " " NAG E 611 " - " ASN E 241 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 386 " " NAG F 609 " - " ASN F 448 " " NAG F 610 " - " ASN F 289 " " NAG F 611 " - " ASN F 241 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 332 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 19.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.831A 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 425 through 429 removed outlier: 4.262A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.246A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' 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 'H' and resid 100I through 102 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.037A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.830A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.262A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.502A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (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 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 636 Processing helix chain 'G' and resid 638 through 663 Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100I through 102 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 4.036A pdb=" N GLU Q 83 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.454A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.830A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.262A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.247A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) 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 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.913A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 636 Processing helix chain 'I' and resid 638 through 663 Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100I through 102 Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.037A pdb=" N GLU R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN A 301 " --> pdb=" O LEU A 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS A 305 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A 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 469 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.930A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.432A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 32 through 39 removed outlier: 7.467A pdb=" N PHE H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP H 34 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100B through 100G Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 11 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95B through 98 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN E 301 " --> pdb=" O LEU E 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS E 305 " --> pdb=" O PHE E 320 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 34 through 39 removed outlier: 6.929A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) 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=AC7, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC8, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.433A 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=AC9, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'O' and resid 32 through 39 removed outlier: 7.466A pdb=" N PHE O 32 " --> pdb=" O ASN O 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN O 52 " --> pdb=" O PHE O 32 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP O 34 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.680A 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 100B through 100G Processing sheet with id=AD2, first strand: chain 'Q' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 11 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 95B through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.258A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.019A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.578A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.110A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 4.009A pdb=" N ASN F 301 " --> pdb=" O LEU F 323A" (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS F 305 " --> pdb=" O PHE F 320 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE F 309 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA F 316 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323A current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'K' and resid 34 through 39 removed outlier: 6.929A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 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: 6.433A 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 'P' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'P' and resid 32 through 39 removed outlier: 7.467A pdb=" N PHE P 32 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN P 52 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP P 34 " --> pdb=" O ASP P 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100B through 100G Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 11 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 95B through 98 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'R' and resid 19 through 24 693 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3921 1.32 - 1.45: 7170 1.45 - 1.58: 13602 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 24891 Sorted by residual: bond pdb=" C PRO R 8 " pdb=" O PRO R 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.99e+01 bond pdb=" C PRO Q 8 " pdb=" O PRO Q 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.96e+01 bond pdb=" C PRO L 8 " pdb=" O PRO L 8 " ideal model delta sigma weight residual 1.246 1.186 0.060 8.50e-03 1.38e+04 4.91e+01 bond pdb=" CA PRO R 8 " pdb=" C PRO R 8 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.04e+01 bond pdb=" CA PRO Q 8 " pdb=" C PRO Q 8 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.02e+01 ... (remaining 24886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 30946 1.80 - 3.59: 2412 3.59 - 5.39: 353 5.39 - 7.19: 45 7.19 - 8.99: 15 Bond angle restraints: 33771 Sorted by residual: angle pdb=" C MET E 161 " pdb=" CA MET E 161 " pdb=" CB MET E 161 " ideal model delta sigma weight residual 116.54 109.29 7.25 1.15e+00 7.56e-01 3.98e+01 angle pdb=" C MET F 161 " pdb=" CA MET F 161 " pdb=" CB MET F 161 " ideal model delta sigma weight residual 116.54 109.29 7.25 1.15e+00 7.56e-01 3.97e+01 angle pdb=" C MET A 161 " pdb=" CA MET A 161 " pdb=" CB MET A 161 " ideal model delta sigma weight residual 116.54 109.30 7.24 1.15e+00 7.56e-01 3.97e+01 angle pdb=" N ARG J 83 " pdb=" CA ARG J 83 " pdb=" C ARG J 83 " ideal model delta sigma weight residual 110.14 101.40 8.74 1.47e+00 4.63e-01 3.53e+01 angle pdb=" N ARG C 83 " pdb=" CA ARG C 83 " pdb=" C ARG C 83 " ideal model delta sigma weight residual 110.14 101.41 8.73 1.47e+00 4.63e-01 3.53e+01 ... (remaining 33766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 14982 21.29 - 42.58: 363 42.58 - 63.86: 141 63.86 - 85.15: 30 85.15 - 106.44: 18 Dihedral angle restraints: 15534 sinusoidal: 6840 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 155.94 -62.94 1 1.00e+01 1.00e-02 5.23e+01 ... (remaining 15531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2850 0.061 - 0.122: 844 0.122 - 0.183: 185 0.183 - 0.243: 12 0.243 - 0.304: 12 Chirality restraints: 3903 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3900 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 477 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C ASP F 477 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP F 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN F 478 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 477 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASP E 477 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP E 477 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN E 478 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 477 " -0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ASP A 477 " 0.060 2.00e-02 2.50e+03 pdb=" O ASP A 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 478 " -0.020 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5356 2.79 - 3.32: 21544 3.32 - 3.85: 41079 3.85 - 4.37: 49003 4.37 - 4.90: 82525 Nonbonded interactions: 199507 Sorted by model distance: nonbonded pdb=" OE1 GLN L 89 " pdb=" NE2 GLN L 96 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLN Q 89 " pdb=" NE2 GLN Q 96 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLN R 89 " pdb=" NE2 GLN R 96 " model vdw 2.269 3.120 nonbonded pdb=" OE2 GLU A 106 " pdb=" NZ LYS B 574 " model vdw 2.283 3.120 nonbonded pdb=" OE2 GLU F 106 " pdb=" NZ LYS I 574 " model vdw 2.283 3.120 ... (remaining 199502 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Z' } 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.800 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.006 0.060 24990 Z= 0.301 Angle : 1.062 9.521 34026 Z= 0.617 Chirality : 0.061 0.304 3903 Planarity : 0.006 0.041 4236 Dihedral : 11.469 106.438 9846 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.34 % Allowed : 1.15 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 2973 helix: 0.30 (0.24), residues: 429 sheet: 1.27 (0.17), residues: 873 loop : 0.64 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 500 TYR 0.019 0.003 TYR Q 36 PHE 0.036 0.003 PHE O 78 TRP 0.025 0.004 TRP H 47 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00617 (24891) covalent geometry : angle 1.04508 (33771) SS BOND : bond 0.00626 ( 42) SS BOND : angle 2.32616 ( 84) hydrogen bonds : bond 0.12695 ( 693) hydrogen bonds : angle 6.34892 ( 1755) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.63375 ( 36) link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.68317 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 764 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8316 (mmtm) REVERT: A 211 GLU cc_start: 0.7573 (tt0) cc_final: 0.7220 (pt0) REVERT: A 217 TYR cc_start: 0.8680 (m-80) cc_final: 0.7849 (m-80) REVERT: C 27 TYR cc_start: 0.7867 (p90) cc_final: 0.7602 (p90) REVERT: C 81 GLN cc_start: 0.8284 (tp40) cc_final: 0.7747 (tp40) REVERT: C 101 ASP cc_start: 0.8032 (t0) cc_final: 0.7768 (t0) REVERT: C 102 PHE cc_start: 0.7549 (m-80) cc_final: 0.7242 (m-80) REVERT: D 21 ILE cc_start: 0.8170 (mt) cc_final: 0.7833 (mp) REVERT: D 27 ILE cc_start: 0.8287 (mm) cc_final: 0.7991 (mm) REVERT: D 69 ASN cc_start: 0.8493 (m-40) cc_final: 0.8290 (m-40) REVERT: B 632 ASP cc_start: 0.8834 (t70) cc_final: 0.8588 (t0) REVERT: H 22 CYS cc_start: 0.5118 (m) cc_final: 0.3898 (m) REVERT: H 60 ASN cc_start: 0.7924 (t0) cc_final: 0.7609 (t0) REVERT: H 66 ARG cc_start: 0.6920 (mtm180) cc_final: 0.6617 (mtm110) REVERT: H 100 MET cc_start: 0.8112 (mmm) cc_final: 0.7747 (mpp) REVERT: L 69 THR cc_start: 0.8328 (p) cc_final: 0.7896 (t) REVERT: L 89 GLN cc_start: 0.7059 (mt0) cc_final: 0.6607 (tt0) REVERT: E 97 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8450 (mmtm) REVERT: E 99 ASN cc_start: 0.8997 (t0) cc_final: 0.8448 (t0) REVERT: E 167 ASP cc_start: 0.7640 (m-30) cc_final: 0.7339 (m-30) REVERT: E 211 GLU cc_start: 0.7667 (tt0) cc_final: 0.7208 (pt0) REVERT: E 302 ASN cc_start: 0.8392 (m-40) cc_final: 0.7917 (m-40) REVERT: E 333 ILE cc_start: 0.8564 (mt) cc_final: 0.8324 (tt) REVERT: E 375 SER cc_start: 0.9061 (t) cc_final: 0.8774 (m) REVERT: E 475 MET cc_start: 0.8294 (mmm) cc_final: 0.7732 (tpp) REVERT: J 81 GLN cc_start: 0.8182 (tp40) cc_final: 0.7689 (tp40) REVERT: M 21 ILE cc_start: 0.8387 (mt) cc_final: 0.8093 (mp) REVERT: M 30 TYR cc_start: 0.8153 (m-80) cc_final: 0.7952 (m-80) REVERT: O 100 GLU cc_start: 0.8129 (pm20) cc_final: 0.7476 (pm20) REVERT: Q 69 THR cc_start: 0.8219 (p) cc_final: 0.7784 (t) REVERT: F 97 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8524 (mmtm) REVERT: F 99 ASN cc_start: 0.8992 (t0) cc_final: 0.8525 (t0) REVERT: F 211 GLU cc_start: 0.7812 (tt0) cc_final: 0.7219 (pt0) REVERT: K 81 GLN cc_start: 0.8171 (tp40) cc_final: 0.7751 (tp40) REVERT: K 101 ASP cc_start: 0.7999 (t0) cc_final: 0.7758 (t0) REVERT: N 91 TYR cc_start: 0.9044 (t80) cc_final: 0.8719 (t80) REVERT: P 60 ASN cc_start: 0.7800 (t0) cc_final: 0.7503 (t0) REVERT: P 66 ARG cc_start: 0.6981 (mtm180) cc_final: 0.6669 (tmm-80) REVERT: P 100 MET cc_start: 0.8174 (mmm) cc_final: 0.7822 (mpp) REVERT: R 27 ASN cc_start: 0.8758 (p0) cc_final: 0.8442 (p0) REVERT: R 69 THR cc_start: 0.8269 (p) cc_final: 0.7872 (t) REVERT: R 89 GLN cc_start: 0.7069 (mt0) cc_final: 0.6725 (tt0) outliers start: 9 outliers final: 3 residues processed: 773 average time/residue: 0.1662 time to fit residues: 200.3289 Evaluate side-chains 532 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.0020 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 425 ASN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 653 GLN L 89 GLN E 170 GLN E 425 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN Q 89 GLN N 6 GLN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113932 restraints weight = 36704.949| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.80 r_work: 0.3318 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24990 Z= 0.158 Angle : 0.696 14.463 34026 Z= 0.358 Chirality : 0.045 0.197 3903 Planarity : 0.004 0.040 4236 Dihedral : 7.371 66.495 4451 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.33 % Allowed : 8.45 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 2973 helix: 1.51 (0.26), residues: 429 sheet: 1.22 (0.17), residues: 867 loop : 0.34 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 617 TYR 0.025 0.001 TYR E 217 PHE 0.021 0.002 PHE O 78 TRP 0.015 0.001 TRP O 33 HIS 0.004 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00374 (24891) covalent geometry : angle 0.65116 (33771) SS BOND : bond 0.00399 ( 42) SS BOND : angle 3.87730 ( 84) hydrogen bonds : bond 0.04512 ( 693) hydrogen bonds : angle 5.33540 ( 1755) link_BETA1-4 : bond 0.00577 ( 12) link_BETA1-4 : angle 2.09943 ( 36) link_NAG-ASN : bond 0.00348 ( 45) link_NAG-ASN : angle 2.36249 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 563 time to evaluate : 0.766 Fit side-chains REVERT: A 97 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8473 (mmtm) REVERT: A 211 GLU cc_start: 0.7999 (tt0) cc_final: 0.7252 (pt0) REVERT: A 215 ILE cc_start: 0.8890 (tp) cc_final: 0.8604 (tp) REVERT: A 217 TYR cc_start: 0.8760 (m-80) cc_final: 0.8049 (m-80) REVERT: A 308 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8047 (mtp85) REVERT: C 81 GLN cc_start: 0.8227 (tp40) cc_final: 0.7573 (tp40) REVERT: C 101 ASP cc_start: 0.8098 (t0) cc_final: 0.7737 (t0) REVERT: D 21 ILE cc_start: 0.8021 (mt) cc_final: 0.7748 (mp) REVERT: D 69 ASN cc_start: 0.8588 (m-40) cc_final: 0.8219 (m110) REVERT: D 91 TYR cc_start: 0.9054 (t80) cc_final: 0.8751 (t80) REVERT: H 3 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6741 (tm-30) REVERT: H 60 ASN cc_start: 0.7995 (t0) cc_final: 0.7622 (t0) REVERT: H 66 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6746 (mtm110) REVERT: H 100 ASP cc_start: 0.8194 (t70) cc_final: 0.7814 (t0) REVERT: H 100 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7475 (mp0) REVERT: H 100 MET cc_start: 0.8207 (mmm) cc_final: 0.7944 (mpp) REVERT: L 53 LYS cc_start: 0.8202 (mttm) cc_final: 0.7885 (mtmm) REVERT: L 89 GLN cc_start: 0.6666 (mt0) cc_final: 0.6298 (tt0) REVERT: E 97 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8556 (mmtm) REVERT: E 104 MET cc_start: 0.8433 (tpt) cc_final: 0.8204 (ttt) REVERT: E 166 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7934 (ttp80) REVERT: E 167 ASP cc_start: 0.7557 (m-30) cc_final: 0.7242 (m-30) REVERT: E 211 GLU cc_start: 0.7932 (tt0) cc_final: 0.7218 (pt0) REVERT: E 230 ASP cc_start: 0.8321 (t0) cc_final: 0.8091 (t0) REVERT: E 333 ILE cc_start: 0.8530 (mt) cc_final: 0.8257 (tt) REVERT: E 375 SER cc_start: 0.8752 (t) cc_final: 0.8431 (m) REVERT: J 81 GLN cc_start: 0.8207 (tp40) cc_final: 0.7544 (tp40) REVERT: M 30 TYR cc_start: 0.8191 (m-80) cc_final: 0.7987 (m-80) REVERT: M 87 TYR cc_start: 0.8281 (m-80) cc_final: 0.8034 (m-80) REVERT: O 60 ASN cc_start: 0.8057 (t0) cc_final: 0.7673 (t0) REVERT: O 81 LYS cc_start: 0.7637 (ttmm) cc_final: 0.6350 (ttpp) REVERT: O 100 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7393 (mp0) REVERT: O 100 MET cc_start: 0.8124 (mpp) cc_final: 0.7853 (mpp) REVERT: Q 53 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7748 (mtmm) REVERT: F 97 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8589 (mmtm) REVERT: F 211 GLU cc_start: 0.8017 (tt0) cc_final: 0.7248 (pt0) REVERT: F 215 ILE cc_start: 0.8833 (tp) cc_final: 0.8572 (tt) REVERT: F 475 MET cc_start: 0.8325 (mmm) cc_final: 0.7804 (tpp) REVERT: K 81 GLN cc_start: 0.8185 (tp40) cc_final: 0.7514 (tp-100) REVERT: I 634 GLU cc_start: 0.7357 (tt0) cc_final: 0.7050 (tt0) REVERT: P 39 GLN cc_start: 0.6888 (pp30) cc_final: 0.6528 (pp30) REVERT: P 60 ASN cc_start: 0.7909 (t0) cc_final: 0.7564 (t0) REVERT: P 66 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6957 (mtm110) REVERT: P 81 LYS cc_start: 0.7947 (tttt) cc_final: 0.7682 (ttpp) REVERT: P 100 MET cc_start: 0.8285 (mmm) cc_final: 0.7920 (mpp) REVERT: R 89 GLN cc_start: 0.6888 (mt0) cc_final: 0.6604 (tt0) outliers start: 87 outliers final: 52 residues processed: 612 average time/residue: 0.1590 time to fit residues: 155.5799 Evaluate side-chains 533 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 481 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 34 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 302 ASN E 422 GLN J 82AHIS M 6 GLN M 69 ASN M 79 GLN Q 89 GLN F 33 ASN ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN F 422 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103099 restraints weight = 37178.923| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.76 r_work: 0.3150 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.121 24990 Z= 0.367 Angle : 0.834 18.099 34026 Z= 0.426 Chirality : 0.051 0.234 3903 Planarity : 0.005 0.038 4236 Dihedral : 6.940 47.727 4450 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 4.51 % Allowed : 10.02 % Favored : 85.47 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 2973 helix: 1.31 (0.26), residues: 411 sheet: 0.59 (0.17), residues: 906 loop : 0.00 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 61 TYR 0.020 0.002 TYR R 87 PHE 0.024 0.003 PHE K 102 TRP 0.040 0.002 TRP C 36 HIS 0.008 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00883 (24891) covalent geometry : angle 0.79735 (33771) SS BOND : bond 0.01306 ( 42) SS BOND : angle 3.74719 ( 84) hydrogen bonds : bond 0.05195 ( 693) hydrogen bonds : angle 5.67270 ( 1755) link_BETA1-4 : bond 0.00525 ( 12) link_BETA1-4 : angle 1.63591 ( 36) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.62320 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 497 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8720 (mmtm) REVERT: A 137 LYS cc_start: 0.8617 (mttp) cc_final: 0.8412 (mttt) REVERT: A 211 GLU cc_start: 0.8176 (tt0) cc_final: 0.7469 (pt0) REVERT: A 217 TYR cc_start: 0.9047 (m-80) cc_final: 0.8017 (m-80) REVERT: A 370 GLU cc_start: 0.7844 (tt0) cc_final: 0.7636 (mp0) REVERT: C 66 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7462 (mtm180) REVERT: C 81 GLN cc_start: 0.8263 (tp40) cc_final: 0.7644 (tp40) REVERT: C 101 ASP cc_start: 0.8679 (t0) cc_final: 0.8291 (t0) REVERT: D 31 ASN cc_start: 0.8908 (p0) cc_final: 0.8697 (p0) REVERT: D 69 ASN cc_start: 0.8975 (m-40) cc_final: 0.8535 (m110) REVERT: B 634 GLU cc_start: 0.7521 (tt0) cc_final: 0.7212 (tt0) REVERT: H 3 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6619 (tm-30) REVERT: H 60 ASN cc_start: 0.8209 (t0) cc_final: 0.7922 (t0) REVERT: H 66 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6777 (mtm110) REVERT: H 100 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7701 (mp0) REVERT: H 100 MET cc_start: 0.8405 (mmm) cc_final: 0.7961 (mpp) REVERT: L 53 LYS cc_start: 0.8479 (mttm) cc_final: 0.8190 (mtmm) REVERT: L 69 THR cc_start: 0.8573 (p) cc_final: 0.8113 (t) REVERT: L 89 GLN cc_start: 0.7009 (mt0) cc_final: 0.6790 (tt0) REVERT: E 97 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8654 (mmtm) REVERT: E 211 GLU cc_start: 0.7998 (tt0) cc_final: 0.7240 (pt0) REVERT: E 296 CYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7577 (t) REVERT: E 333 ILE cc_start: 0.8785 (mt) cc_final: 0.8428 (tt) REVERT: E 370 GLU cc_start: 0.7900 (tt0) cc_final: 0.7653 (mt-10) REVERT: E 375 SER cc_start: 0.9146 (t) cc_final: 0.8831 (m) REVERT: E 475 MET cc_start: 0.8367 (mmm) cc_final: 0.7990 (tpp) REVERT: J 81 GLN cc_start: 0.8078 (tp40) cc_final: 0.7315 (tp40) REVERT: M 31 ASN cc_start: 0.8849 (p0) cc_final: 0.8630 (p0) REVERT: M 32 TYR cc_start: 0.9125 (m-80) cc_final: 0.8861 (m-80) REVERT: O 39 GLN cc_start: 0.7048 (pt0) cc_final: 0.6593 (pp30) REVERT: O 60 ASN cc_start: 0.8178 (t0) cc_final: 0.7825 (t0) REVERT: Q 53 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8118 (mtmm) REVERT: Q 60 ASP cc_start: 0.8702 (t0) cc_final: 0.8450 (m-30) REVERT: Q 69 THR cc_start: 0.8518 (p) cc_final: 0.8045 (t) REVERT: F 97 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8771 (mmtm) REVERT: F 117 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8297 (tptt) REVERT: F 215 ILE cc_start: 0.8995 (tp) cc_final: 0.8693 (tt) REVERT: F 296 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7290 (t) REVERT: F 370 GLU cc_start: 0.7957 (tt0) cc_final: 0.7539 (mp0) REVERT: K 81 GLN cc_start: 0.8115 (tp40) cc_final: 0.7694 (tp40) REVERT: P 39 GLN cc_start: 0.7211 (pp30) cc_final: 0.6708 (pp30) REVERT: P 60 ASN cc_start: 0.8091 (t0) cc_final: 0.7730 (t0) REVERT: P 66 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6837 (mtm110) REVERT: P 100 GLU cc_start: 0.9034 (pm20) cc_final: 0.8601 (pm20) REVERT: R 69 THR cc_start: 0.8451 (p) cc_final: 0.8014 (t) outliers start: 118 outliers final: 79 residues processed: 573 average time/residue: 0.1607 time to fit residues: 146.5368 Evaluate side-chains 545 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 464 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 613 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 268 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 39 optimal weight: 0.0870 chunk 144 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 279 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 188 ASN A 422 GLN D 79 GLN E 188 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 302 ASN F 422 GLN K 82AHIS N 6 GLN N 39 HIS N 69 ASN I 543 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106062 restraints weight = 36393.015| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.72 r_work: 0.3220 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24990 Z= 0.141 Angle : 0.643 12.197 34026 Z= 0.328 Chirality : 0.044 0.194 3903 Planarity : 0.004 0.039 4236 Dihedral : 5.750 38.902 4446 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.36 % Allowed : 13.00 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 2973 helix: 1.83 (0.27), residues: 411 sheet: 0.62 (0.17), residues: 900 loop : -0.05 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.015 0.001 TYR D 91 PHE 0.019 0.002 PHE K 102 TRP 0.018 0.001 TRP C 36 HIS 0.005 0.001 HIS K 82A Details of bonding type rmsd covalent geometry : bond 0.00334 (24891) covalent geometry : angle 0.61162 (33771) SS BOND : bond 0.00505 ( 42) SS BOND : angle 2.86132 ( 84) hydrogen bonds : bond 0.03974 ( 693) hydrogen bonds : angle 5.17863 ( 1755) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.46595 ( 36) link_NAG-ASN : bond 0.00215 ( 45) link_NAG-ASN : angle 2.19382 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 496 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8665 (mmtm) REVERT: A 141 MET cc_start: 0.8116 (ptp) cc_final: 0.7652 (ptp) REVERT: A 211 GLU cc_start: 0.8132 (tt0) cc_final: 0.7415 (pt0) REVERT: A 217 TYR cc_start: 0.8845 (m-80) cc_final: 0.7954 (m-80) REVERT: A 328 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7883 (ttm) REVERT: A 492 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 27 TYR cc_start: 0.8020 (p90) cc_final: 0.7749 (p90) REVERT: C 36 TRP cc_start: 0.8852 (m100) cc_final: 0.8577 (m100) REVERT: C 66 ARG cc_start: 0.7712 (mtm180) cc_final: 0.7372 (mtm180) REVERT: D 31 ASN cc_start: 0.8932 (p0) cc_final: 0.8702 (p0) REVERT: D 69 ASN cc_start: 0.8900 (m-40) cc_final: 0.8426 (m110) REVERT: B 634 GLU cc_start: 0.7376 (tt0) cc_final: 0.7081 (tt0) REVERT: H 60 ASN cc_start: 0.8103 (t0) cc_final: 0.7769 (t0) REVERT: H 66 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6741 (mtm110) REVERT: H 100 MET cc_start: 0.8263 (mmm) cc_final: 0.8052 (mpp) REVERT: H 105 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7639 (mm-40) REVERT: L 53 LYS cc_start: 0.8339 (mttm) cc_final: 0.8037 (mtmm) REVERT: L 69 THR cc_start: 0.8578 (p) cc_final: 0.8140 (t) REVERT: L 89 GLN cc_start: 0.6887 (mt0) cc_final: 0.6576 (tt0) REVERT: E 97 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8619 (mmtm) REVERT: E 117 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8267 (tptt) REVERT: E 166 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.8157 (ttp80) REVERT: E 323 LEU cc_start: 0.8642 (mt) cc_final: 0.8436 (mt) REVERT: E 333 ILE cc_start: 0.8869 (mt) cc_final: 0.8508 (tt) REVERT: E 375 SER cc_start: 0.9092 (t) cc_final: 0.8787 (m) REVERT: E 475 MET cc_start: 0.8191 (mmm) cc_final: 0.7901 (tpp) REVERT: J 81 GLN cc_start: 0.8144 (tp40) cc_final: 0.7395 (tp40) REVERT: M 31 ASN cc_start: 0.8846 (p0) cc_final: 0.8545 (p0) REVERT: O 39 GLN cc_start: 0.7041 (pt0) cc_final: 0.6770 (pp30) REVERT: O 60 ASN cc_start: 0.8110 (t0) cc_final: 0.7723 (t0) REVERT: O 81 LYS cc_start: 0.7621 (ttmm) cc_final: 0.6401 (ttpp) REVERT: O 100 GLU cc_start: 0.8787 (pm20) cc_final: 0.8351 (pm20) REVERT: O 105 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7751 (mm-40) REVERT: Q 53 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8096 (mtmm) REVERT: Q 60 ASP cc_start: 0.8590 (t0) cc_final: 0.8373 (m-30) REVERT: Q 69 THR cc_start: 0.8500 (p) cc_final: 0.8049 (t) REVERT: F 51 THR cc_start: 0.9262 (m) cc_final: 0.8897 (p) REVERT: F 97 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8737 (mmtm) REVERT: F 117 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8317 (tptt) REVERT: F 370 GLU cc_start: 0.7859 (tt0) cc_final: 0.7430 (mp0) REVERT: F 475 MET cc_start: 0.8012 (tpp) cc_final: 0.7762 (tpp) REVERT: K 81 GLN cc_start: 0.8137 (tp40) cc_final: 0.7570 (tp40) REVERT: K 91 TYR cc_start: 0.9026 (m-80) cc_final: 0.8703 (m-80) REVERT: P 39 GLN cc_start: 0.7349 (pp30) cc_final: 0.6781 (pp30) REVERT: P 60 ASN cc_start: 0.8032 (t0) cc_final: 0.7644 (t0) REVERT: P 68 THR cc_start: 0.8500 (m) cc_final: 0.8234 (m) REVERT: P 81 LYS cc_start: 0.8023 (tttt) cc_final: 0.7617 (ttpp) REVERT: P 100 GLU cc_start: 0.8896 (pm20) cc_final: 0.8317 (pm20) REVERT: R 69 THR cc_start: 0.8471 (p) cc_final: 0.8031 (t) REVERT: R 89 GLN cc_start: 0.7800 (tt0) cc_final: 0.7553 (tt0) REVERT: R 95 SER cc_start: 0.8720 (m) cc_final: 0.8274 (p) outliers start: 88 outliers final: 69 residues processed: 546 average time/residue: 0.1630 time to fit residues: 140.3361 Evaluate side-chains 534 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 464 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 234 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 216 HIS E 302 ASN E 348 GLN M 39 HIS ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 37 GLN N 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101489 restraints weight = 36998.485| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.78 r_work: 0.3161 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 24990 Z= 0.311 Angle : 0.726 12.365 34026 Z= 0.369 Chirality : 0.048 0.225 3903 Planarity : 0.004 0.041 4236 Dihedral : 5.950 44.508 4446 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.13 % Allowed : 13.42 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.15), residues: 2973 helix: 1.47 (0.26), residues: 411 sheet: 0.41 (0.17), residues: 924 loop : -0.20 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 61 TYR 0.019 0.002 TYR M 32 PHE 0.018 0.002 PHE K 102 TRP 0.014 0.002 TRP O 33 HIS 0.006 0.002 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00751 (24891) covalent geometry : angle 0.69411 (33771) SS BOND : bond 0.00647 ( 42) SS BOND : angle 3.04238 ( 84) hydrogen bonds : bond 0.04579 ( 693) hydrogen bonds : angle 5.39795 ( 1755) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.49753 ( 36) link_NAG-ASN : bond 0.00425 ( 45) link_NAG-ASN : angle 2.40922 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 471 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8735 (mmtm) REVERT: A 211 GLU cc_start: 0.8198 (tt0) cc_final: 0.7458 (pt0) REVERT: A 217 TYR cc_start: 0.8826 (m-80) cc_final: 0.7930 (m-80) REVERT: A 328 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8064 (ttm) REVERT: C 36 TRP cc_start: 0.8831 (m100) cc_final: 0.8520 (m100) REVERT: D 31 ASN cc_start: 0.9012 (p0) cc_final: 0.8703 (p0) REVERT: D 45 LYS cc_start: 0.8188 (tttt) cc_final: 0.7921 (pttp) REVERT: D 69 ASN cc_start: 0.8962 (m-40) cc_final: 0.8443 (m110) REVERT: D 79 GLN cc_start: 0.6832 (pt0) cc_final: 0.6286 (pp30) REVERT: D 82 ASP cc_start: 0.6400 (m-30) cc_final: 0.5731 (m-30) REVERT: H 60 ASN cc_start: 0.8151 (t0) cc_final: 0.7852 (t0) REVERT: H 66 ARG cc_start: 0.7355 (mtm180) cc_final: 0.6954 (mtm110) REVERT: H 100 GLU cc_start: 0.7887 (mp0) cc_final: 0.7617 (mp0) REVERT: H 100 MET cc_start: 0.8351 (mmm) cc_final: 0.8099 (mpp) REVERT: L 53 LYS cc_start: 0.8495 (mttm) cc_final: 0.8149 (mtmm) REVERT: L 69 THR cc_start: 0.8618 (p) cc_final: 0.8198 (t) REVERT: L 89 GLN cc_start: 0.7026 (mt0) cc_final: 0.6780 (tt0) REVERT: E 97 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8666 (mmtm) REVERT: E 117 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8302 (tptt) REVERT: E 333 ILE cc_start: 0.8878 (mt) cc_final: 0.8467 (tt) REVERT: E 370 GLU cc_start: 0.7873 (tt0) cc_final: 0.7670 (mt-10) REVERT: E 375 SER cc_start: 0.9199 (t) cc_final: 0.8858 (m) REVERT: E 475 MET cc_start: 0.8299 (mmm) cc_final: 0.7984 (tpp) REVERT: J 81 GLN cc_start: 0.8135 (tp40) cc_final: 0.7269 (tp40) REVERT: M 31 ASN cc_start: 0.8940 (p0) cc_final: 0.8591 (p0) REVERT: O 39 GLN cc_start: 0.7160 (pt0) cc_final: 0.6677 (pp30) REVERT: O 60 ASN cc_start: 0.8172 (t0) cc_final: 0.7801 (t0) REVERT: O 100 GLU cc_start: 0.8864 (pm20) cc_final: 0.8437 (pm20) REVERT: Q 53 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8103 (mtmm) REVERT: Q 60 ASP cc_start: 0.8613 (t0) cc_final: 0.8410 (m-30) REVERT: Q 69 THR cc_start: 0.8514 (p) cc_final: 0.7996 (t) REVERT: F 51 THR cc_start: 0.9321 (m) cc_final: 0.8973 (p) REVERT: F 97 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8801 (mmtm) REVERT: F 111 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8119 (tt) REVERT: F 202 THR cc_start: 0.8967 (m) cc_final: 0.8740 (t) REVERT: F 370 GLU cc_start: 0.7993 (tt0) cc_final: 0.7606 (mp0) REVERT: F 423 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9065 (mp) REVERT: K 81 GLN cc_start: 0.8227 (tp40) cc_final: 0.7498 (tp40) REVERT: K 91 TYR cc_start: 0.9036 (m-80) cc_final: 0.8677 (m-80) REVERT: P 39 GLN cc_start: 0.7232 (pp30) cc_final: 0.6561 (pp30) REVERT: P 60 ASN cc_start: 0.8048 (t0) cc_final: 0.7666 (t0) REVERT: P 68 THR cc_start: 0.8547 (m) cc_final: 0.8331 (m) REVERT: P 81 LYS cc_start: 0.8122 (tttt) cc_final: 0.7704 (ttpp) REVERT: P 100 GLU cc_start: 0.8978 (pm20) cc_final: 0.8385 (pm20) REVERT: P 100 GLU cc_start: 0.7801 (mp0) cc_final: 0.7453 (mp0) REVERT: R 69 THR cc_start: 0.8551 (p) cc_final: 0.8075 (t) REVERT: R 95 SER cc_start: 0.8758 (m) cc_final: 0.8324 (p) outliers start: 108 outliers final: 91 residues processed: 535 average time/residue: 0.1374 time to fit residues: 118.1217 Evaluate side-chains 545 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 451 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 109 VAL Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 259 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 0.0470 chunk 216 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS M 79 GLN ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS R 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104655 restraints weight = 36882.972| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.81 r_work: 0.3218 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24990 Z= 0.144 Angle : 0.615 9.575 34026 Z= 0.311 Chirality : 0.044 0.182 3903 Planarity : 0.004 0.045 4236 Dihedral : 5.468 39.155 4446 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.59 % Allowed : 14.53 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 2973 helix: 1.77 (0.27), residues: 411 sheet: 0.46 (0.17), residues: 903 loop : -0.18 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 66 TYR 0.014 0.001 TYR M 32 PHE 0.017 0.001 PHE H 78 TRP 0.013 0.001 TRP O 36 HIS 0.004 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00346 (24891) covalent geometry : angle 0.59173 (33771) SS BOND : bond 0.00452 ( 42) SS BOND : angle 2.22444 ( 84) hydrogen bonds : bond 0.03860 ( 693) hydrogen bonds : angle 5.12867 ( 1755) link_BETA1-4 : bond 0.00360 ( 12) link_BETA1-4 : angle 1.30582 ( 36) link_NAG-ASN : bond 0.00208 ( 45) link_NAG-ASN : angle 2.07329 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 463 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8642 (mmtm) REVERT: A 166 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7418 (ttp-110) REVERT: A 213 ILE cc_start: 0.8397 (tt) cc_final: 0.8122 (tt) REVERT: A 217 TYR cc_start: 0.8538 (m-80) cc_final: 0.7996 (m-80) REVERT: A 308 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8227 (mtp-110) REVERT: A 328 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7947 (ttm) REVERT: A 492 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 36 TRP cc_start: 0.8715 (m100) cc_final: 0.8495 (m100) REVERT: D 31 ASN cc_start: 0.8936 (p0) cc_final: 0.8562 (p0) REVERT: D 42 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7908 (pttp) REVERT: D 45 LYS cc_start: 0.7982 (tttt) cc_final: 0.7775 (pttp) REVERT: D 69 ASN cc_start: 0.8898 (m-40) cc_final: 0.8418 (m110) REVERT: B 634 GLU cc_start: 0.7064 (tt0) cc_final: 0.6857 (tt0) REVERT: H 60 ASN cc_start: 0.8119 (t0) cc_final: 0.7842 (t0) REVERT: H 66 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6933 (mtm110) REVERT: H 90 TYR cc_start: 0.7491 (m-10) cc_final: 0.7268 (m-10) REVERT: H 100 MET cc_start: 0.8302 (mmm) cc_final: 0.8079 (mpp) REVERT: L 53 LYS cc_start: 0.8331 (mttm) cc_final: 0.8033 (mtmm) REVERT: L 69 THR cc_start: 0.8550 (p) cc_final: 0.8170 (t) REVERT: E 51 THR cc_start: 0.9371 (m) cc_final: 0.8956 (p) REVERT: E 97 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8578 (mmtm) REVERT: E 117 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8275 (tptt) REVERT: E 333 ILE cc_start: 0.8806 (mt) cc_final: 0.8488 (tt) REVERT: E 375 SER cc_start: 0.9033 (t) cc_final: 0.8716 (m) REVERT: E 475 MET cc_start: 0.7997 (mmm) cc_final: 0.7653 (tpp) REVERT: J 81 GLN cc_start: 0.8194 (tp40) cc_final: 0.7343 (tp40) REVERT: M 31 ASN cc_start: 0.8895 (p0) cc_final: 0.8559 (p0) REVERT: M 45 LYS cc_start: 0.7963 (tttm) cc_final: 0.7677 (tmmt) REVERT: O 58 ASN cc_start: 0.8030 (m-40) cc_final: 0.7822 (m-40) REVERT: O 60 ASN cc_start: 0.8131 (t0) cc_final: 0.7738 (t0) REVERT: O 81 LYS cc_start: 0.7736 (ttmm) cc_final: 0.6531 (ttpp) REVERT: O 100 GLU cc_start: 0.8712 (pm20) cc_final: 0.8287 (pm20) REVERT: Q 53 LYS cc_start: 0.8314 (mtmm) cc_final: 0.8020 (mtmm) REVERT: Q 69 THR cc_start: 0.8432 (p) cc_final: 0.7940 (t) REVERT: F 51 THR cc_start: 0.9261 (m) cc_final: 0.8984 (p) REVERT: F 97 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8712 (mmtm) REVERT: F 111 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8115 (tt) REVERT: F 117 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8303 (tptt) REVERT: F 370 GLU cc_start: 0.7728 (tt0) cc_final: 0.7478 (mp0) REVERT: K 81 GLN cc_start: 0.8267 (tp40) cc_final: 0.7576 (tp40) REVERT: N 103 ARG cc_start: 0.8701 (tpt170) cc_final: 0.7788 (mmp-170) REVERT: P 39 GLN cc_start: 0.7355 (pp30) cc_final: 0.6693 (pp30) REVERT: P 60 ASN cc_start: 0.8022 (t0) cc_final: 0.7642 (t0) REVERT: P 100 GLU cc_start: 0.8692 (pm20) cc_final: 0.8004 (pm20) REVERT: P 100 GLU cc_start: 0.7693 (mp0) cc_final: 0.7330 (mp0) REVERT: R 69 THR cc_start: 0.8538 (p) cc_final: 0.8114 (t) REVERT: R 95 SER cc_start: 0.8713 (m) cc_final: 0.8265 (p) outliers start: 94 outliers final: 73 residues processed: 517 average time/residue: 0.1675 time to fit residues: 137.1960 Evaluate side-chains 530 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 455 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN L 89 GLN L 96 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN Q 27BASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 39 HIS R 34 GLN R 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104553 restraints weight = 36737.925| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.77 r_work: 0.3191 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24990 Z= 0.172 Angle : 0.616 9.858 34026 Z= 0.312 Chirality : 0.044 0.195 3903 Planarity : 0.004 0.046 4236 Dihedral : 5.365 38.981 4446 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 14.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 2973 helix: 1.75 (0.26), residues: 411 sheet: 0.39 (0.17), residues: 888 loop : -0.19 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 61 TYR 0.012 0.001 TYR H 91 PHE 0.016 0.002 PHE O 78 TRP 0.013 0.001 TRP O 36 HIS 0.005 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00418 (24891) covalent geometry : angle 0.59106 (33771) SS BOND : bond 0.00512 ( 42) SS BOND : angle 2.28907 ( 84) hydrogen bonds : bond 0.03898 ( 693) hydrogen bonds : angle 5.12982 ( 1755) link_BETA1-4 : bond 0.00356 ( 12) link_BETA1-4 : angle 1.28159 ( 36) link_NAG-ASN : bond 0.00250 ( 45) link_NAG-ASN : angle 2.09892 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 469 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.9176 (m) cc_final: 0.8877 (p) REVERT: A 97 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8738 (mmtm) REVERT: A 166 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7945 (ttp80) REVERT: A 202 THR cc_start: 0.8879 (m) cc_final: 0.8669 (t) REVERT: A 217 TYR cc_start: 0.8749 (m-80) cc_final: 0.7977 (m-80) REVERT: A 303 THR cc_start: 0.8631 (t) cc_final: 0.8406 (p) REVERT: A 308 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8394 (mtp-110) REVERT: A 328 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8082 (ttm) REVERT: A 492 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 36 TRP cc_start: 0.8798 (m100) cc_final: 0.8581 (m100) REVERT: D 31 ASN cc_start: 0.9049 (p0) cc_final: 0.8673 (p0) REVERT: D 42 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8035 (pttp) REVERT: D 69 ASN cc_start: 0.8927 (m-40) cc_final: 0.8383 (m110) REVERT: D 79 GLN cc_start: 0.6816 (pt0) cc_final: 0.6195 (pp30) REVERT: D 82 ASP cc_start: 0.6591 (m-30) cc_final: 0.5924 (m-30) REVERT: D 103 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8223 (mmp-170) REVERT: B 634 GLU cc_start: 0.7462 (tt0) cc_final: 0.7227 (tt0) REVERT: H 60 ASN cc_start: 0.8065 (t0) cc_final: 0.7790 (t0) REVERT: H 66 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6897 (mtm110) REVERT: H 90 TYR cc_start: 0.7584 (m-10) cc_final: 0.7326 (m-10) REVERT: H 100 MET cc_start: 0.8314 (mmm) cc_final: 0.8077 (mpp) REVERT: L 34 GLN cc_start: 0.8264 (mt0) cc_final: 0.8012 (mt0) REVERT: L 53 LYS cc_start: 0.8406 (mttm) cc_final: 0.8073 (mtmm) REVERT: L 69 THR cc_start: 0.8574 (p) cc_final: 0.8183 (t) REVERT: L 89 GLN cc_start: 0.7261 (tt0) cc_final: 0.6849 (tt0) REVERT: E 51 THR cc_start: 0.9392 (m) cc_final: 0.9015 (p) REVERT: E 97 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8681 (mmtm) REVERT: E 117 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8274 (tptt) REVERT: E 328 MET cc_start: 0.8384 (ttm) cc_final: 0.7765 (ttp) REVERT: E 333 ILE cc_start: 0.8887 (mt) cc_final: 0.8566 (tt) REVERT: E 375 SER cc_start: 0.9133 (t) cc_final: 0.8790 (m) REVERT: E 475 MET cc_start: 0.8110 (mmm) cc_final: 0.7723 (tpp) REVERT: J 81 GLN cc_start: 0.8355 (tp40) cc_final: 0.7347 (tp40) REVERT: M 31 ASN cc_start: 0.8980 (p0) cc_final: 0.8603 (p0) REVERT: M 45 LYS cc_start: 0.8057 (tttm) cc_final: 0.7624 (tmmt) REVERT: M 79 GLN cc_start: 0.6649 (pt0) cc_final: 0.6279 (pp30) REVERT: O 58 ASN cc_start: 0.8038 (m-40) cc_final: 0.7825 (m-40) REVERT: O 60 ASN cc_start: 0.8107 (t0) cc_final: 0.7703 (t0) REVERT: O 81 LYS cc_start: 0.7713 (ttmm) cc_final: 0.6513 (ttpp) REVERT: O 100 GLU cc_start: 0.8810 (pm20) cc_final: 0.8391 (pm20) REVERT: Q 53 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8061 (mtmm) REVERT: Q 60 ASP cc_start: 0.8656 (t0) cc_final: 0.8434 (m-30) REVERT: Q 69 THR cc_start: 0.8442 (p) cc_final: 0.7916 (t) REVERT: F 51 THR cc_start: 0.9316 (m) cc_final: 0.9051 (p) REVERT: F 97 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8778 (mmtm) REVERT: F 106 GLU cc_start: 0.8245 (tt0) cc_final: 0.8034 (tt0) REVERT: F 111 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8140 (tt) REVERT: F 117 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8332 (tptt) REVERT: F 202 THR cc_start: 0.8932 (m) cc_final: 0.8719 (t) REVERT: F 370 GLU cc_start: 0.7988 (tt0) cc_final: 0.7508 (mp0) REVERT: F 475 MET cc_start: 0.7829 (tpp) cc_final: 0.7559 (tpp) REVERT: K 81 GLN cc_start: 0.8478 (tp40) cc_final: 0.7721 (tp40) REVERT: N 66 LYS cc_start: 0.8455 (tttm) cc_final: 0.8169 (tttm) REVERT: N 103 ARG cc_start: 0.8690 (tpt170) cc_final: 0.8472 (mmp-170) REVERT: P 60 ASN cc_start: 0.8010 (t0) cc_final: 0.7622 (t0) REVERT: P 100 GLU cc_start: 0.8816 (pm20) cc_final: 0.8185 (pm20) REVERT: P 100 GLU cc_start: 0.7806 (mp0) cc_final: 0.7475 (mp0) REVERT: R 69 THR cc_start: 0.8569 (p) cc_final: 0.8103 (t) REVERT: R 95 SER cc_start: 0.8753 (m) cc_final: 0.8333 (p) outliers start: 96 outliers final: 84 residues processed: 527 average time/residue: 0.1697 time to fit residues: 142.1062 Evaluate side-chains 533 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 447 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 97 optimal weight: 0.0670 chunk 191 optimal weight: 0.4980 chunk 195 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82AHIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.110166 restraints weight = 37247.968| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.68 r_work: 0.3188 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24990 Z= 0.192 Angle : 0.633 10.102 34026 Z= 0.319 Chirality : 0.045 0.199 3903 Planarity : 0.004 0.050 4236 Dihedral : 5.412 39.758 4446 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.59 % Allowed : 14.49 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.15), residues: 2973 helix: 1.68 (0.26), residues: 411 sheet: 0.30 (0.17), residues: 897 loop : -0.23 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.014 0.001 TYR N 32 PHE 0.016 0.002 PHE A 53 TRP 0.013 0.001 TRP O 36 HIS 0.005 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00464 (24891) covalent geometry : angle 0.60825 (33771) SS BOND : bond 0.00464 ( 42) SS BOND : angle 2.28048 ( 84) hydrogen bonds : bond 0.03956 ( 693) hydrogen bonds : angle 5.17085 ( 1755) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 1.26870 ( 36) link_NAG-ASN : bond 0.00292 ( 45) link_NAG-ASN : angle 2.17230 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 461 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9243 (m) cc_final: 0.8964 (p) REVERT: A 97 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8753 (mmtm) REVERT: A 217 TYR cc_start: 0.8740 (m-80) cc_final: 0.8025 (m-80) REVERT: A 328 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: A 375 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8953 (p) REVERT: C 36 TRP cc_start: 0.8804 (m100) cc_final: 0.8598 (m100) REVERT: D 31 ASN cc_start: 0.9072 (p0) cc_final: 0.8696 (p0) REVERT: D 42 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8070 (pttp) REVERT: D 69 ASN cc_start: 0.8943 (m-40) cc_final: 0.8374 (m110) REVERT: H 39 GLN cc_start: 0.6996 (pp30) cc_final: 0.6573 (pp30) REVERT: H 60 ASN cc_start: 0.7994 (t0) cc_final: 0.7731 (t0) REVERT: H 66 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6947 (mtm110) REVERT: H 100 MET cc_start: 0.8357 (mmm) cc_final: 0.8116 (mpp) REVERT: L 53 LYS cc_start: 0.8422 (mttm) cc_final: 0.8101 (mtmm) REVERT: L 66 GLN cc_start: 0.8549 (tt0) cc_final: 0.8250 (tt0) REVERT: L 69 THR cc_start: 0.8544 (p) cc_final: 0.8118 (t) REVERT: L 89 GLN cc_start: 0.7594 (tt0) cc_final: 0.7216 (tt0) REVERT: L 96 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: E 51 THR cc_start: 0.9394 (m) cc_final: 0.9034 (p) REVERT: E 97 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8680 (mmtm) REVERT: E 117 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8312 (tptt) REVERT: E 303 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8355 (p) REVERT: E 328 MET cc_start: 0.8433 (ttm) cc_final: 0.7722 (ttp) REVERT: E 333 ILE cc_start: 0.8889 (mt) cc_final: 0.8558 (tt) REVERT: E 375 SER cc_start: 0.9140 (t) cc_final: 0.8793 (m) REVERT: E 475 MET cc_start: 0.8125 (mmm) cc_final: 0.7772 (tpp) REVERT: J 81 GLN cc_start: 0.8466 (tp40) cc_final: 0.7423 (tp40) REVERT: M 31 ASN cc_start: 0.9004 (p0) cc_final: 0.8620 (p0) REVERT: M 45 LYS cc_start: 0.8051 (tttm) cc_final: 0.7648 (tmmt) REVERT: O 60 ASN cc_start: 0.8129 (t0) cc_final: 0.7730 (t0) REVERT: O 81 LYS cc_start: 0.7795 (ttmm) cc_final: 0.6596 (ttpp) REVERT: O 100 GLU cc_start: 0.8801 (pm20) cc_final: 0.8387 (pm20) REVERT: Q 53 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8107 (mtmm) REVERT: Q 69 THR cc_start: 0.8465 (p) cc_final: 0.7936 (t) REVERT: F 97 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8782 (mmtm) REVERT: F 106 GLU cc_start: 0.8254 (tt0) cc_final: 0.8024 (tt0) REVERT: F 111 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8100 (tt) REVERT: F 117 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8346 (tptt) REVERT: F 202 THR cc_start: 0.8940 (m) cc_final: 0.8738 (t) REVERT: F 370 GLU cc_start: 0.7980 (tt0) cc_final: 0.7531 (mp0) REVERT: F 440 GLN cc_start: 0.8221 (tp40) cc_final: 0.7787 (tp-100) REVERT: K 23 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8207 (tpp-160) REVERT: K 81 GLN cc_start: 0.8552 (tp40) cc_final: 0.7559 (tp40) REVERT: K 82 MET cc_start: 0.8261 (mmm) cc_final: 0.7778 (mmm) REVERT: N 66 LYS cc_start: 0.8454 (tttm) cc_final: 0.8192 (tttp) REVERT: N 103 ARG cc_start: 0.8703 (tpt170) cc_final: 0.8478 (mmp-170) REVERT: P 60 ASN cc_start: 0.8029 (t0) cc_final: 0.7395 (t0) REVERT: P 100 GLU cc_start: 0.8823 (pm20) cc_final: 0.8251 (pm20) REVERT: P 100 GLU cc_start: 0.7866 (mp0) cc_final: 0.7563 (mp0) REVERT: R 69 THR cc_start: 0.8608 (p) cc_final: 0.8149 (t) REVERT: R 95 SER cc_start: 0.8782 (m) cc_final: 0.8346 (p) outliers start: 94 outliers final: 85 residues processed: 521 average time/residue: 0.1705 time to fit residues: 140.6920 Evaluate side-chains 536 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 446 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 293 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS D 79 GLN L 89 GLN M 79 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109676 restraints weight = 37277.214| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.72 r_work: 0.3205 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24990 Z= 0.145 Angle : 0.610 10.943 34026 Z= 0.308 Chirality : 0.044 0.238 3903 Planarity : 0.004 0.050 4236 Dihedral : 5.269 39.257 4446 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.25 % Allowed : 15.18 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 2973 helix: 1.78 (0.26), residues: 411 sheet: 0.32 (0.18), residues: 897 loop : -0.22 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 66 TYR 0.014 0.001 TYR R 91 PHE 0.018 0.001 PHE O 78 TRP 0.014 0.001 TRP O 36 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00351 (24891) covalent geometry : angle 0.58816 (33771) SS BOND : bond 0.00439 ( 42) SS BOND : angle 2.11216 ( 84) hydrogen bonds : bond 0.03744 ( 693) hydrogen bonds : angle 5.08365 ( 1755) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.24169 ( 36) link_NAG-ASN : bond 0.00298 ( 45) link_NAG-ASN : angle 2.04343 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 457 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9259 (m) cc_final: 0.9038 (p) REVERT: A 97 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 217 TYR cc_start: 0.8688 (m-80) cc_final: 0.8024 (m-80) REVERT: A 328 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8073 (ttm) REVERT: A 375 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8908 (p) REVERT: A 490 LYS cc_start: 0.8876 (tttp) cc_final: 0.8630 (tttm) REVERT: C 27 TYR cc_start: 0.8051 (p90) cc_final: 0.7809 (p90) REVERT: D 31 ASN cc_start: 0.9078 (p0) cc_final: 0.8699 (p0) REVERT: D 42 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8068 (pttp) REVERT: D 69 ASN cc_start: 0.8888 (m-40) cc_final: 0.8291 (m110) REVERT: D 79 GLN cc_start: 0.6749 (pt0) cc_final: 0.6146 (pp30) REVERT: B 634 GLU cc_start: 0.7447 (tt0) cc_final: 0.7170 (tt0) REVERT: H 60 ASN cc_start: 0.7953 (t0) cc_final: 0.7689 (t0) REVERT: H 66 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6931 (mtm110) REVERT: H 90 TYR cc_start: 0.7559 (m-10) cc_final: 0.7354 (m-10) REVERT: H 100 MET cc_start: 0.8342 (mmm) cc_final: 0.8098 (mpp) REVERT: L 53 LYS cc_start: 0.8402 (mttm) cc_final: 0.8089 (mtmm) REVERT: L 66 GLN cc_start: 0.8555 (tt0) cc_final: 0.8283 (tt0) REVERT: L 69 THR cc_start: 0.8513 (p) cc_final: 0.8111 (t) REVERT: E 51 THR cc_start: 0.9392 (m) cc_final: 0.9094 (p) REVERT: E 97 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8682 (mmtm) REVERT: E 106 GLU cc_start: 0.8264 (tt0) cc_final: 0.7969 (tt0) REVERT: E 117 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8307 (tptt) REVERT: E 161 MET cc_start: 0.7985 (tpt) cc_final: 0.7782 (tpt) REVERT: E 328 MET cc_start: 0.8396 (ttm) cc_final: 0.7699 (ttp) REVERT: E 333 ILE cc_start: 0.8821 (mt) cc_final: 0.8532 (tt) REVERT: E 375 SER cc_start: 0.9099 (t) cc_final: 0.8752 (m) REVERT: E 475 MET cc_start: 0.8150 (mmm) cc_final: 0.7841 (tpp) REVERT: J 81 GLN cc_start: 0.8527 (tp40) cc_final: 0.7514 (tp40) REVERT: M 31 ASN cc_start: 0.8998 (p0) cc_final: 0.8622 (p0) REVERT: M 45 LYS cc_start: 0.7963 (tttm) cc_final: 0.7622 (tmmt) REVERT: M 79 GLN cc_start: 0.6776 (pt0) cc_final: 0.6402 (pp30) REVERT: M 103 ARG cc_start: 0.8482 (mmp-170) cc_final: 0.7552 (mmp-170) REVERT: O 60 ASN cc_start: 0.8144 (t0) cc_final: 0.7772 (t0) REVERT: O 81 LYS cc_start: 0.7770 (ttmm) cc_final: 0.6574 (ttpp) REVERT: O 100 GLU cc_start: 0.8781 (pm20) cc_final: 0.8359 (pm20) REVERT: Q 6 THR cc_start: 0.7950 (m) cc_final: 0.7285 (p) REVERT: Q 53 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8076 (mtmm) REVERT: Q 69 THR cc_start: 0.8428 (p) cc_final: 0.7927 (t) REVERT: F 97 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8785 (mmtm) REVERT: F 106 GLU cc_start: 0.8253 (tt0) cc_final: 0.8026 (tt0) REVERT: F 111 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (tt) REVERT: F 117 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8347 (tptt) REVERT: F 370 GLU cc_start: 0.7946 (tt0) cc_final: 0.7496 (mp0) REVERT: F 440 GLN cc_start: 0.8217 (tp40) cc_final: 0.7759 (tp-100) REVERT: K 81 GLN cc_start: 0.8584 (tp40) cc_final: 0.7578 (tp40) REVERT: K 82 MET cc_start: 0.8297 (mmm) cc_final: 0.7906 (mmm) REVERT: N 30 TYR cc_start: 0.8871 (m-80) cc_final: 0.8669 (m-80) REVERT: N 45 LYS cc_start: 0.8195 (pttp) cc_final: 0.7903 (ptmm) REVERT: N 103 ARG cc_start: 0.8695 (tpt170) cc_final: 0.8475 (mmp-170) REVERT: P 60 ASN cc_start: 0.8010 (t0) cc_final: 0.7370 (t0) REVERT: P 100 GLU cc_start: 0.8810 (pm20) cc_final: 0.8248 (pm20) REVERT: P 100 GLU cc_start: 0.7838 (mp0) cc_final: 0.7545 (mp0) REVERT: R 69 THR cc_start: 0.8590 (p) cc_final: 0.8138 (t) REVERT: R 95 SER cc_start: 0.8766 (m) cc_final: 0.8359 (p) outliers start: 85 outliers final: 77 residues processed: 513 average time/residue: 0.1635 time to fit residues: 133.1859 Evaluate side-chains 524 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 444 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 100 GLU Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 146 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 190 optimal weight: 0.0670 chunk 148 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 276 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109246 restraints weight = 36777.467| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.69 r_work: 0.3251 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24990 Z= 0.120 Angle : 0.647 17.650 34026 Z= 0.325 Chirality : 0.045 0.313 3903 Planarity : 0.004 0.052 4236 Dihedral : 5.157 38.490 4446 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.10 % Allowed : 15.63 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 2973 helix: 2.20 (0.27), residues: 393 sheet: 0.38 (0.18), residues: 897 loop : -0.24 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 66 TYR 0.013 0.001 TYR N 32 PHE 0.019 0.001 PHE H 78 TRP 0.051 0.001 TRP C 36 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00278 (24891) covalent geometry : angle 0.61770 (33771) SS BOND : bond 0.00436 ( 42) SS BOND : angle 2.87961 ( 84) hydrogen bonds : bond 0.03532 ( 693) hydrogen bonds : angle 4.97358 ( 1755) link_BETA1-4 : bond 0.00377 ( 12) link_BETA1-4 : angle 1.15987 ( 36) link_NAG-ASN : bond 0.00224 ( 45) link_NAG-ASN : angle 2.09350 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 469 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8760 (mmtm) REVERT: A 217 TYR cc_start: 0.8618 (m-80) cc_final: 0.8141 (m-80) REVERT: A 328 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8006 (ttm) REVERT: A 375 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 490 LYS cc_start: 0.8877 (tttp) cc_final: 0.8645 (tttm) REVERT: D 26 THR cc_start: 0.8061 (p) cc_final: 0.7857 (m) REVERT: D 31 ASN cc_start: 0.9087 (p0) cc_final: 0.8722 (p0) REVERT: D 69 ASN cc_start: 0.8859 (m-40) cc_final: 0.8303 (m110) REVERT: B 634 GLU cc_start: 0.7331 (tt0) cc_final: 0.7074 (tt0) REVERT: H 60 ASN cc_start: 0.7938 (t0) cc_final: 0.7689 (t0) REVERT: H 66 ARG cc_start: 0.7297 (mtm180) cc_final: 0.6897 (mtm110) REVERT: H 100 MET cc_start: 0.8351 (mmm) cc_final: 0.8102 (mpp) REVERT: L 53 LYS cc_start: 0.8412 (mttm) cc_final: 0.8139 (mtmm) REVERT: L 66 GLN cc_start: 0.8512 (tt0) cc_final: 0.8278 (tt0) REVERT: L 69 THR cc_start: 0.8541 (p) cc_final: 0.8148 (t) REVERT: L 95 SER cc_start: 0.8572 (m) cc_final: 0.7995 (p) REVERT: E 51 THR cc_start: 0.9355 (m) cc_final: 0.9126 (p) REVERT: E 97 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8676 (mmtm) REVERT: E 106 GLU cc_start: 0.8268 (tt0) cc_final: 0.7895 (tt0) REVERT: E 117 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8332 (tptt) REVERT: E 328 MET cc_start: 0.8380 (ttm) cc_final: 0.7656 (ttp) REVERT: E 333 ILE cc_start: 0.8971 (mt) cc_final: 0.8632 (tt) REVERT: E 375 SER cc_start: 0.9033 (t) cc_final: 0.8709 (m) REVERT: E 440 GLN cc_start: 0.8129 (tp40) cc_final: 0.7623 (tp-100) REVERT: E 475 MET cc_start: 0.8077 (mmm) cc_final: 0.7763 (tpp) REVERT: J 81 GLN cc_start: 0.8580 (tp40) cc_final: 0.7595 (tp40) REVERT: M 31 ASN cc_start: 0.8980 (p0) cc_final: 0.8625 (p0) REVERT: M 45 LYS cc_start: 0.7975 (tttm) cc_final: 0.7629 (tmmt) REVERT: M 79 GLN cc_start: 0.6694 (pt0) cc_final: 0.6236 (tm-30) REVERT: O 81 LYS cc_start: 0.7746 (ttmm) cc_final: 0.6562 (ttpp) REVERT: O 100 GLU cc_start: 0.8742 (pm20) cc_final: 0.8319 (pm20) REVERT: Q 6 THR cc_start: 0.7930 (m) cc_final: 0.7272 (p) REVERT: Q 53 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8057 (mtmm) REVERT: Q 69 THR cc_start: 0.8396 (p) cc_final: 0.7895 (t) REVERT: F 97 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8792 (mmtm) REVERT: F 106 GLU cc_start: 0.8251 (tt0) cc_final: 0.8028 (tt0) REVERT: F 117 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8361 (tptt) REVERT: F 370 GLU cc_start: 0.7933 (tt0) cc_final: 0.7512 (mp0) REVERT: F 440 GLN cc_start: 0.8194 (tp40) cc_final: 0.7752 (tp-100) REVERT: K 81 GLN cc_start: 0.8589 (tp40) cc_final: 0.7610 (tp40) REVERT: K 82 MET cc_start: 0.8280 (mmm) cc_final: 0.7970 (mmm) REVERT: N 45 LYS cc_start: 0.8189 (pttp) cc_final: 0.7834 (ptmm) REVERT: P 60 ASN cc_start: 0.8014 (t0) cc_final: 0.7393 (t0) REVERT: P 100 GLU cc_start: 0.8780 (pm20) cc_final: 0.8242 (pm20) REVERT: P 100 GLU cc_start: 0.7824 (mp0) cc_final: 0.7561 (mp0) REVERT: R 35 TRP cc_start: 0.7419 (m100) cc_final: 0.7201 (m100) REVERT: R 69 THR cc_start: 0.8600 (p) cc_final: 0.8157 (t) REVERT: R 95 SER cc_start: 0.8747 (m) cc_final: 0.8346 (p) REVERT: R 102 THR cc_start: 0.5331 (p) cc_final: 0.4803 (p) outliers start: 81 outliers final: 71 residues processed: 521 average time/residue: 0.1666 time to fit residues: 137.7664 Evaluate side-chains 523 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 450 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 295 ASN Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 184 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 229 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN M 6 GLN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.106274 restraints weight = 36591.128| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.70 r_work: 0.3224 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24990 Z= 0.144 Angle : 0.668 19.453 34026 Z= 0.334 Chirality : 0.045 0.326 3903 Planarity : 0.004 0.050 4236 Dihedral : 5.195 38.927 4446 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.98 % Allowed : 15.79 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2973 helix: 2.19 (0.27), residues: 393 sheet: 0.41 (0.18), residues: 897 loop : -0.24 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 66 TYR 0.016 0.001 TYR N 32 PHE 0.017 0.001 PHE O 78 TRP 0.036 0.001 TRP C 36 HIS 0.006 0.001 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00339 (24891) covalent geometry : angle 0.63693 (33771) SS BOND : bond 0.00565 ( 42) SS BOND : angle 3.21592 ( 84) hydrogen bonds : bond 0.03609 ( 693) hydrogen bonds : angle 4.96972 ( 1755) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.20109 ( 36) link_NAG-ASN : bond 0.00213 ( 45) link_NAG-ASN : angle 2.04168 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.68 seconds wall clock time: 125 minutes 8.53 seconds (7508.53 seconds total)