Starting phenix.real_space_refine on Fri May 23 13:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4l_41035/05_2025/8t4l_41035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4l_41035/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4l_41035/05_2025/8t4l_41035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4l_41035/05_2025/8t4l_41035.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4l_41035/05_2025/8t4l_41035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4l_41035/05_2025/8t4l_41035.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.82, per 1000 atoms: 0.65 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: 6.40 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.16 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: 8.05 Time building geometry restraints manager: 7.39 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: 0.13 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: 2.690 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: 0.040 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.050 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.170 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.410 ------------------------------------------------------------------------------- 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 : 2.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.025 0.004 TRP H 47 HIS 0.008 0.002 HIS A 374 PHE 0.036 0.003 PHE O 78 TYR 0.019 0.003 TYR Q 36 ARG 0.006 0.001 ARG F 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.68317 ( 135) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 1.63375 ( 36) hydrogen bonds : bond 0.12695 ( 693) hydrogen bonds : angle 6.34892 ( 1755) SS BOND : bond 0.00626 ( 42) SS BOND : angle 2.32616 ( 84) covalent geometry : bond 0.00617 (24891) covalent geometry : angle 1.04508 (33771) *********************** 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 : 2.767 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: 0.7746 (tp40) REVERT: C 101 ASP cc_start: 0.8032 (t0) cc_final: 0.7769 (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: 0.7832 (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: 0.3899 (m) REVERT: H 60 ASN cc_start: 0.7924 (t0) cc_final: 0.7608 (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: 0.7900 (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: 0.8451 (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: 0.8773 (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: 0.7690 (tp40) REVERT: M 21 ILE cc_start: 0.8387 (mt) cc_final: 0.8093 (mp) REVERT: O 100 GLU cc_start: 0.8129 (pm20) cc_final: 0.7477 (pm20) REVERT: Q 69 THR cc_start: 0.8219 (p) cc_final: 0.7789 (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: 0.7220 (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: 0.8443 (p0) REVERT: R 69 THR cc_start: 0.8269 (p) cc_final: 0.7878 (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: 0.3533 time to fit residues: 424.5868 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 : 2.561 ------------------------------------------------------------------------------- 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 248 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 230 optimal weight: 0.0370 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.145333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112564 restraints weight = 36491.369| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.79 r_work: 0.3298 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24990 Z= 0.175 Angle : 0.708 14.162 34026 Z= 0.366 Chirality : 0.045 0.196 3903 Planarity : 0.004 0.038 4236 Dihedral : 7.500 67.902 4451 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.29 % Allowed : 8.60 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 2973 helix: 1.48 (0.26), residues: 429 sheet: 1.24 (0.17), residues: 903 loop : 0.35 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 33 HIS 0.005 0.001 HIS N 39 PHE 0.020 0.002 PHE O 78 TYR 0.024 0.002 TYR E 217 ARG 0.006 0.001 ARG G 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 2.42810 ( 135) link_BETA1-4 : bond 0.00559 ( 12) link_BETA1-4 : angle 2.03412 ( 36) hydrogen bonds : bond 0.04663 ( 693) hydrogen bonds : angle 5.37422 ( 1755) SS BOND : bond 0.00505 ( 42) SS BOND : angle 3.74398 ( 84) covalent geometry : bond 0.00418 (24891) covalent geometry : angle 0.66496 (33771) *********************** 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 639 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 553 time to evaluate : 2.646 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8482 (mmtm) REVERT: A 211 GLU cc_start: 0.8004 (tt0) cc_final: 0.7257 (pt0) REVERT: A 215 ILE cc_start: 0.8902 (tp) cc_final: 0.8613 (tp) REVERT: A 217 TYR cc_start: 0.8794 (m-80) cc_final: 0.8109 (m-80) REVERT: A 308 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8000 (mtp85) REVERT: C 81 GLN cc_start: 0.8260 (tp40) cc_final: 0.7615 (tp40) REVERT: C 101 ASP cc_start: 0.8090 (t0) cc_final: 0.7742 (t0) REVERT: D 21 ILE cc_start: 0.8023 (mt) cc_final: 0.7752 (mp) REVERT: D 69 ASN cc_start: 0.8592 (m-40) cc_final: 0.8175 (m110) REVERT: D 91 TYR cc_start: 0.9081 (t80) cc_final: 0.8789 (t80) REVERT: H 3 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6785 (tm-30) REVERT: H 60 ASN cc_start: 0.8001 (t0) cc_final: 0.7637 (t0) REVERT: H 66 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6748 (mtm110) REVERT: H 100 ASP cc_start: 0.8235 (t70) cc_final: 0.7882 (t0) REVERT: H 100 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7488 (mp0) REVERT: H 100 MET cc_start: 0.8201 (mmm) cc_final: 0.7932 (mpp) REVERT: L 53 LYS cc_start: 0.8243 (mttm) cc_final: 0.7910 (mtmm) REVERT: L 89 GLN cc_start: 0.6709 (mt0) cc_final: 0.6337 (tt0) REVERT: E 97 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8514 (mmtm) REVERT: E 211 GLU cc_start: 0.7937 (tt0) cc_final: 0.7212 (pt0) REVERT: E 333 ILE cc_start: 0.8527 (mt) cc_final: 0.8265 (tt) REVERT: E 375 SER cc_start: 0.8773 (t) cc_final: 0.8443 (m) REVERT: J 81 GLN cc_start: 0.8202 (tp40) cc_final: 0.7581 (tp40) REVERT: O 60 ASN cc_start: 0.8051 (t0) cc_final: 0.7678 (t0) REVERT: O 100 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7306 (mp0) REVERT: Q 53 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7775 (mtmm) REVERT: F 97 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8612 (mmtm) REVERT: F 211 GLU cc_start: 0.8016 (tt0) cc_final: 0.7243 (pt0) REVERT: F 215 ILE cc_start: 0.8852 (tp) cc_final: 0.8583 (tt) REVERT: F 217 TYR cc_start: 0.8817 (m-80) cc_final: 0.8597 (m-80) REVERT: F 347 LYS cc_start: 0.7984 (pttm) cc_final: 0.7774 (ptmt) REVERT: F 475 MET cc_start: 0.8299 (mmm) cc_final: 0.7806 (tpp) REVERT: K 81 GLN cc_start: 0.8186 (tp40) cc_final: 0.7520 (tp-100) REVERT: I 634 GLU cc_start: 0.7356 (tt0) cc_final: 0.7049 (tt0) REVERT: P 39 GLN cc_start: 0.6883 (pp30) cc_final: 0.6561 (pp30) REVERT: P 60 ASN cc_start: 0.7923 (t0) cc_final: 0.7574 (t0) REVERT: P 66 ARG cc_start: 0.7232 (mtm180) cc_final: 0.6955 (mtm110) REVERT: P 81 LYS cc_start: 0.7973 (tttt) cc_final: 0.7704 (ttpp) REVERT: P 100 MET cc_start: 0.8296 (mmm) cc_final: 0.7942 (mpp) REVERT: R 89 GLN cc_start: 0.6920 (mt0) cc_final: 0.6657 (tt0) outliers start: 86 outliers final: 53 residues processed: 603 average time/residue: 0.3334 time to fit residues: 319.9822 Evaluate side-chains 528 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 475 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 272 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 269 GLU 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 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 165 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 6 GLN M 69 ASN M 79 GLN N 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108926 restraints weight = 36502.923| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.76 r_work: 0.3242 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24990 Z= 0.198 Angle : 0.696 15.255 34026 Z= 0.355 Chirality : 0.045 0.205 3903 Planarity : 0.004 0.034 4236 Dihedral : 6.216 43.308 4450 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.56 % Allowed : 10.09 % Favored : 86.35 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 2973 helix: 1.75 (0.27), residues: 417 sheet: 0.85 (0.17), residues: 906 loop : 0.15 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.005 0.001 HIS J 82A PHE 0.023 0.002 PHE K 102 TYR 0.019 0.002 TYR R 87 ARG 0.004 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 45) link_NAG-ASN : angle 2.18208 ( 135) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.69278 ( 36) hydrogen bonds : bond 0.04324 ( 693) hydrogen bonds : angle 5.25022 ( 1755) SS BOND : bond 0.00539 ( 42) SS BOND : angle 3.65136 ( 84) covalent geometry : bond 0.00475 (24891) covalent geometry : angle 0.65781 (33771) *********************** 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 609 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 516 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8545 (mmtm) REVERT: A 211 GLU cc_start: 0.8044 (tt0) cc_final: 0.7357 (pt0) REVERT: A 217 TYR cc_start: 0.8818 (m-80) cc_final: 0.7933 (m-80) REVERT: C 66 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7365 (mtm180) REVERT: C 81 GLN cc_start: 0.8262 (tp40) cc_final: 0.7530 (tp40) REVERT: C 101 ASP cc_start: 0.8362 (t0) cc_final: 0.7996 (t0) REVERT: D 21 ILE cc_start: 0.8177 (mt) cc_final: 0.7900 (mp) REVERT: D 69 ASN cc_start: 0.8884 (m-40) cc_final: 0.8486 (m110) REVERT: D 91 TYR cc_start: 0.9148 (t80) cc_final: 0.8748 (t80) REVERT: B 634 GLU cc_start: 0.7175 (tt0) cc_final: 0.6870 (tt0) REVERT: H 3 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6720 (tm-30) REVERT: H 60 ASN cc_start: 0.8121 (t0) cc_final: 0.7795 (t0) REVERT: H 66 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6857 (mtm110) REVERT: H 100 ASP cc_start: 0.8124 (t0) cc_final: 0.7748 (m-30) REVERT: H 100 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7635 (mp0) REVERT: H 100 MET cc_start: 0.8323 (mmm) cc_final: 0.7891 (mpp) REVERT: L 53 LYS cc_start: 0.8292 (mttm) cc_final: 0.8032 (mtmm) REVERT: L 89 GLN cc_start: 0.6790 (mt0) cc_final: 0.6541 (tt0) REVERT: E 97 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8513 (mmtm) REVERT: E 141 MET cc_start: 0.8018 (mtt) cc_final: 0.7743 (mtt) REVERT: E 211 GLU cc_start: 0.7971 (tt0) cc_final: 0.7256 (pt0) REVERT: E 333 ILE cc_start: 0.8727 (mt) cc_final: 0.8410 (tt) REVERT: E 375 SER cc_start: 0.8889 (t) cc_final: 0.8566 (m) REVERT: E 475 MET cc_start: 0.8218 (mmm) cc_final: 0.7936 (tpp) REVERT: J 81 GLN cc_start: 0.8070 (tp40) cc_final: 0.7496 (tp40) REVERT: O 39 GLN cc_start: 0.6953 (pt0) cc_final: 0.6582 (pp30) REVERT: O 60 ASN cc_start: 0.8085 (t0) cc_final: 0.7697 (t0) REVERT: O 81 LYS cc_start: 0.7671 (ttmm) cc_final: 0.6504 (ttpp) REVERT: O 100 ASP cc_start: 0.8365 (t0) cc_final: 0.7951 (m-30) REVERT: Q 53 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7987 (mtmm) REVERT: Q 69 THR cc_start: 0.8442 (p) cc_final: 0.7999 (t) REVERT: F 97 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8654 (mmtm) REVERT: F 112 TRP cc_start: 0.8591 (t-100) cc_final: 0.8311 (t-100) REVERT: F 211 GLU cc_start: 0.8031 (tt0) cc_final: 0.7235 (pt0) REVERT: F 215 ILE cc_start: 0.8796 (tp) cc_final: 0.8537 (tt) REVERT: F 370 GLU cc_start: 0.7512 (tt0) cc_final: 0.7311 (mp0) REVERT: F 475 MET cc_start: 0.8339 (mmm) cc_final: 0.8058 (tpp) REVERT: F 492 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8108 (mt-10) REVERT: K 45 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8049 (pp) REVERT: K 81 GLN cc_start: 0.8044 (tp40) cc_final: 0.7658 (tp40) REVERT: N 6 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6277 (mt0) REVERT: N 79 GLN cc_start: 0.7096 (pt0) cc_final: 0.6787 (pp30) REVERT: P 39 GLN cc_start: 0.7218 (pp30) cc_final: 0.6731 (pp30) REVERT: P 60 ASN cc_start: 0.8029 (t0) cc_final: 0.7663 (t0) REVERT: P 66 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6820 (mtm110) REVERT: P 100 GLU cc_start: 0.8924 (pm20) cc_final: 0.8568 (pm20) REVERT: P 100 MET cc_start: 0.8366 (mmm) cc_final: 0.8044 (mpp) REVERT: R 89 GLN cc_start: 0.7039 (mt0) cc_final: 0.6767 (tt0) outliers start: 93 outliers final: 64 residues processed: 574 average time/residue: 0.3413 time to fit residues: 309.1278 Evaluate side-chains 538 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 472 time to evaluate : 2.536 ------------------------------------------------------------------------------- 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 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 368 ASP Chi-restraints excluded: chain A residue 375 SER 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 D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 615 SER 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 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 132 THR 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 322 ASP 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 28 THR Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN 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 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 150 MET 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 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 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL 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 206 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 111 optimal weight: 0.0470 chunk 293 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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 D 31 ASN D 79 GLN E 188 ASN J 82AHIS M 6 GLN M 79 GLN ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN F 348 GLN N 69 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107185 restraints weight = 36941.029| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.77 r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 24990 Z= 0.185 Angle : 0.643 11.943 34026 Z= 0.329 Chirality : 0.045 0.204 3903 Planarity : 0.004 0.036 4236 Dihedral : 5.554 38.227 4446 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.75 % Allowed : 11.31 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2973 helix: 1.83 (0.27), residues: 411 sheet: 0.73 (0.17), residues: 906 loop : 0.02 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 36 HIS 0.006 0.001 HIS K 82A PHE 0.019 0.002 PHE K 102 TYR 0.017 0.002 TYR H 91 ARG 0.008 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 45) link_NAG-ASN : angle 2.18942 ( 135) link_BETA1-4 : bond 0.00389 ( 12) link_BETA1-4 : angle 1.50459 ( 36) hydrogen bonds : bond 0.04043 ( 693) hydrogen bonds : angle 5.08145 ( 1755) SS BOND : bond 0.00588 ( 42) SS BOND : angle 2.76155 ( 84) covalent geometry : bond 0.00447 (24891) covalent geometry : angle 0.61366 (33771) *********************** 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 588 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 490 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8692 (mmtm) REVERT: A 141 MET cc_start: 0.8138 (ptp) cc_final: 0.7893 (ptp) REVERT: A 211 GLU cc_start: 0.8113 (tt0) cc_final: 0.7404 (pt0) REVERT: A 217 TYR cc_start: 0.8836 (m-80) cc_final: 0.7907 (m-80) REVERT: C 66 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7380 (mtm180) REVERT: C 81 GLN cc_start: 0.8332 (tp40) cc_final: 0.7589 (tp40) REVERT: D 69 ASN cc_start: 0.8936 (m-40) cc_final: 0.8496 (m110) REVERT: D 79 GLN cc_start: 0.6824 (pt0) cc_final: 0.6362 (pp30) REVERT: D 82 ASP cc_start: 0.6032 (m-30) cc_final: 0.5360 (m-30) REVERT: D 91 TYR cc_start: 0.9208 (t80) cc_final: 0.9002 (t80) REVERT: B 634 GLU cc_start: 0.7602 (tt0) cc_final: 0.7301 (tt0) REVERT: H 60 ASN cc_start: 0.8077 (t0) cc_final: 0.7749 (t0) REVERT: H 66 ARG cc_start: 0.7179 (mtm180) cc_final: 0.6758 (mtm110) REVERT: H 100 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: H 105 GLN cc_start: 0.8139 (mp10) cc_final: 0.7934 (mm-40) REVERT: L 53 LYS cc_start: 0.8344 (mttm) cc_final: 0.8063 (mtmm) REVERT: L 69 THR cc_start: 0.8551 (p) cc_final: 0.8113 (t) REVERT: L 89 GLN cc_start: 0.6867 (mt0) cc_final: 0.6521 (tt0) REVERT: E 97 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8625 (mmtm) REVERT: E 117 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8219 (tptt) REVERT: E 211 GLU cc_start: 0.8044 (tt0) cc_final: 0.7316 (pt0) REVERT: E 333 ILE cc_start: 0.8874 (mt) cc_final: 0.8523 (tt) REVERT: E 375 SER cc_start: 0.9054 (t) cc_final: 0.8753 (m) REVERT: J 81 GLN cc_start: 0.8094 (tp40) cc_final: 0.7440 (tp40) REVERT: M 6 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6233 (tt0) REVERT: M 37 GLN cc_start: 0.8561 (tt0) cc_final: 0.7987 (tt0) REVERT: M 45 LYS cc_start: 0.8091 (tttt) cc_final: 0.7888 (tttt) REVERT: O 39 GLN cc_start: 0.7004 (pt0) cc_final: 0.6746 (pp30) REVERT: O 60 ASN cc_start: 0.8112 (t0) cc_final: 0.7719 (t0) REVERT: O 81 LYS cc_start: 0.7679 (ttmm) cc_final: 0.6466 (ttpp) REVERT: O 100 GLU cc_start: 0.8798 (pm20) cc_final: 0.8270 (pm20) REVERT: O 105 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7759 (mm-40) REVERT: Q 53 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7961 (mtmm) REVERT: Q 69 THR cc_start: 0.8455 (p) cc_final: 0.8025 (t) REVERT: F 51 THR cc_start: 0.9265 (m) cc_final: 0.8981 (p) REVERT: F 54 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6728 (p) REVERT: F 97 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8775 (mmtm) REVERT: F 106 GLU cc_start: 0.8209 (tt0) cc_final: 0.7989 (tt0) REVERT: F 112 TRP cc_start: 0.8658 (t-100) cc_final: 0.8405 (t-100) REVERT: F 117 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8374 (tptt) REVERT: F 370 GLU cc_start: 0.7795 (tt0) cc_final: 0.7442 (mp0) REVERT: F 475 MET cc_start: 0.8317 (mmm) cc_final: 0.8051 (tpp) REVERT: K 81 GLN cc_start: 0.8083 (tp40) cc_final: 0.7497 (tp40) REVERT: N 45 LYS cc_start: 0.8092 (tttt) cc_final: 0.7822 (ttpt) REVERT: P 39 GLN cc_start: 0.7292 (pp30) cc_final: 0.6709 (pp30) REVERT: P 60 ASN cc_start: 0.8056 (t0) cc_final: 0.7672 (t0) REVERT: P 66 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6808 (mtm110) REVERT: P 81 LYS cc_start: 0.8003 (tttt) cc_final: 0.7707 (ttpp) REVERT: P 100 GLU cc_start: 0.8991 (pm20) cc_final: 0.8395 (pm20) REVERT: P 100 MET cc_start: 0.8392 (mmm) cc_final: 0.8183 (mpp) REVERT: R 69 THR cc_start: 0.8542 (p) cc_final: 0.8079 (t) REVERT: R 89 GLN cc_start: 0.6987 (mt0) cc_final: 0.6742 (tt0) outliers start: 98 outliers final: 77 residues processed: 547 average time/residue: 0.3420 time to fit residues: 297.6872 Evaluate side-chains 542 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 462 time to evaluate : 2.920 ------------------------------------------------------------------------------- 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 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 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 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 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 100 GLU 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 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 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 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 J residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 26 THR 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 G residue 625 ASN 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 F residue 54 CYS 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 167 ASP 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 303 THR 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 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 47 MET 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 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 197 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN D 6 GLN D 31 ASN E 422 GLN M 6 GLN ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106135 restraints weight = 36620.112| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.74 r_work: 0.3221 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24990 Z= 0.169 Angle : 0.625 11.700 34026 Z= 0.317 Chirality : 0.044 0.192 3903 Planarity : 0.004 0.038 4236 Dihedral : 5.358 38.425 4446 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.90 % Allowed : 12.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 2973 helix: 1.89 (0.27), residues: 411 sheet: 0.68 (0.17), residues: 930 loop : -0.06 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 36 HIS 0.005 0.001 HIS D 39 PHE 0.024 0.002 PHE F 53 TYR 0.015 0.001 TYR M 32 ARG 0.005 0.000 ARG N 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 45) link_NAG-ASN : angle 2.12676 ( 135) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.38817 ( 36) hydrogen bonds : bond 0.03872 ( 693) hydrogen bonds : angle 5.00282 ( 1755) SS BOND : bond 0.00390 ( 42) SS BOND : angle 2.56507 ( 84) covalent geometry : bond 0.00407 (24891) covalent geometry : angle 0.59724 (33771) *********************** 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 571 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 469 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8697 (mmtm) REVERT: A 141 MET cc_start: 0.8147 (ptp) cc_final: 0.7733 (ptp) REVERT: A 211 GLU cc_start: 0.8097 (tt0) cc_final: 0.7382 (pt0) REVERT: A 217 TYR cc_start: 0.8702 (m-80) cc_final: 0.7963 (m-80) REVERT: A 308 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8475 (mtp-110) REVERT: A 328 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7970 (ttm) REVERT: A 492 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 69 ASN cc_start: 0.8940 (m-40) cc_final: 0.8458 (m110) REVERT: D 91 TYR cc_start: 0.9218 (t80) cc_final: 0.8987 (t80) REVERT: B 634 GLU cc_start: 0.7509 (tt0) cc_final: 0.7170 (tt0) REVERT: H 60 ASN cc_start: 0.8070 (t0) cc_final: 0.7765 (t0) REVERT: H 66 ARG cc_start: 0.7156 (mtm180) cc_final: 0.6741 (mtm110) REVERT: H 100 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: L 53 LYS cc_start: 0.8335 (mttm) cc_final: 0.8060 (mtmm) REVERT: L 69 THR cc_start: 0.8536 (p) cc_final: 0.8064 (t) REVERT: L 89 GLN cc_start: 0.6850 (mt0) cc_final: 0.6586 (tt0) REVERT: E 97 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8632 (mmtm) REVERT: E 117 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8241 (tptt) REVERT: E 211 GLU cc_start: 0.8009 (tt0) cc_final: 0.7261 (pt0) REVERT: E 333 ILE cc_start: 0.8855 (mt) cc_final: 0.8520 (tt) REVERT: E 375 SER cc_start: 0.9094 (t) cc_final: 0.8790 (m) REVERT: E 475 MET cc_start: 0.7931 (tpp) cc_final: 0.7690 (tpp) REVERT: J 81 GLN cc_start: 0.8115 (tp40) cc_final: 0.7390 (tp40) REVERT: M 45 LYS cc_start: 0.8145 (tttt) cc_final: 0.7900 (tttt) REVERT: O 39 GLN cc_start: 0.6981 (pt0) cc_final: 0.6734 (pp30) REVERT: O 58 ASN cc_start: 0.8005 (m-40) cc_final: 0.7796 (m-40) REVERT: O 60 ASN cc_start: 0.8084 (t0) cc_final: 0.7686 (t0) REVERT: O 81 LYS cc_start: 0.7683 (ttmm) cc_final: 0.6428 (ttpp) REVERT: O 100 GLU cc_start: 0.8763 (pm20) cc_final: 0.8303 (pm20) REVERT: O 105 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7819 (mm-40) REVERT: Q 53 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7987 (mtmm) REVERT: Q 69 THR cc_start: 0.8433 (p) cc_final: 0.7977 (t) REVERT: F 51 THR cc_start: 0.9254 (m) cc_final: 0.8957 (p) REVERT: F 97 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8758 (mmtm) REVERT: F 106 GLU cc_start: 0.8189 (tt0) cc_final: 0.7969 (tt0) REVERT: F 117 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8356 (tptt) REVERT: F 370 GLU cc_start: 0.7837 (tt0) cc_final: 0.7439 (mp0) REVERT: F 475 MET cc_start: 0.8186 (mmm) cc_final: 0.7928 (tpp) REVERT: K 81 GLN cc_start: 0.8101 (tp40) cc_final: 0.7483 (tp40) REVERT: N 79 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6572 (pp30) REVERT: N 82 ASP cc_start: 0.6569 (m-30) cc_final: 0.6258 (m-30) REVERT: P 39 GLN cc_start: 0.7351 (pp30) cc_final: 0.6720 (pp30) REVERT: P 60 ASN cc_start: 0.8067 (t0) cc_final: 0.7684 (t0) REVERT: P 66 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6771 (mtm110) REVERT: P 81 LYS cc_start: 0.7954 (tttt) cc_final: 0.7586 (ttpp) REVERT: P 100 GLU cc_start: 0.8941 (pm20) cc_final: 0.8359 (pm20) REVERT: R 69 THR cc_start: 0.8520 (p) cc_final: 0.8057 (t) REVERT: R 89 GLN cc_start: 0.6955 (mt0) cc_final: 0.6710 (tt0) outliers start: 102 outliers final: 77 residues processed: 531 average time/residue: 0.3369 time to fit residues: 284.6057 Evaluate side-chains 541 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 461 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 C residue 2 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 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 100 GLU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 58 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 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 434 MET 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 G residue 544 LEU Chi-restraints excluded: chain G residue 620 SER Chi-restraints excluded: chain G residue 625 ASN 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 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 188 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 303 THR 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 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 N residue 79 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 164 optimal weight: 0.0980 chunk 67 optimal weight: 0.0000 chunk 108 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 275 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 218 optimal weight: 0.0980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN M 39 HIS M 79 GLN ** Q 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109150 restraints weight = 36267.868| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.73 r_work: 0.3265 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24990 Z= 0.111 Angle : 0.586 12.039 34026 Z= 0.297 Chirality : 0.043 0.202 3903 Planarity : 0.004 0.041 4236 Dihedral : 5.097 37.598 4446 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.25 % Allowed : 13.49 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2973 helix: 2.07 (0.27), residues: 411 sheet: 0.79 (0.17), residues: 870 loop : -0.08 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 36 HIS 0.003 0.001 HIS A 330 PHE 0.017 0.001 PHE O 78 TYR 0.014 0.001 TYR F 191 ARG 0.008 0.000 ARG Q 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 45) link_NAG-ASN : angle 1.94449 ( 135) link_BETA1-4 : bond 0.00415 ( 12) link_BETA1-4 : angle 1.31085 ( 36) hydrogen bonds : bond 0.03501 ( 693) hydrogen bonds : angle 4.84706 ( 1755) SS BOND : bond 0.00442 ( 42) SS BOND : angle 2.03882 ( 84) covalent geometry : bond 0.00258 (24891) covalent geometry : angle 0.56486 (33771) *********************** 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 555 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 470 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8318 (mp10) cc_final: 0.7970 (mp10) REVERT: A 97 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8685 (mmtm) REVERT: A 141 MET cc_start: 0.8012 (ptp) cc_final: 0.7618 (ptp) REVERT: A 211 GLU cc_start: 0.8026 (tt0) cc_final: 0.7271 (pt0) REVERT: A 308 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8465 (mtp-110) REVERT: A 328 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: A 492 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8002 (mt-10) REVERT: D 45 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7514 (pttp) REVERT: D 69 ASN cc_start: 0.8933 (m-40) cc_final: 0.8466 (m110) REVERT: D 79 GLN cc_start: 0.6839 (pt0) cc_final: 0.6265 (pp30) REVERT: D 82 ASP cc_start: 0.6334 (m-30) cc_final: 0.5651 (m-30) REVERT: D 91 TYR cc_start: 0.9174 (t80) cc_final: 0.8659 (t80) REVERT: B 634 GLU cc_start: 0.7463 (tt0) cc_final: 0.7165 (tt0) REVERT: H 39 GLN cc_start: 0.7150 (pp30) cc_final: 0.6914 (pp30) REVERT: H 45 LEU cc_start: 0.6792 (mt) cc_final: 0.6527 (mt) REVERT: H 60 ASN cc_start: 0.8032 (t0) cc_final: 0.7710 (t0) REVERT: H 66 ARG cc_start: 0.7140 (mtm180) cc_final: 0.6725 (mtm110) REVERT: L 53 LYS cc_start: 0.8253 (mttm) cc_final: 0.7986 (mtmm) REVERT: L 69 THR cc_start: 0.8501 (p) cc_final: 0.8081 (t) REVERT: L 89 GLN cc_start: 0.6809 (mt0) cc_final: 0.6551 (tt0) REVERT: E 97 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8626 (mmtm) REVERT: E 117 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8235 (tptt) REVERT: E 141 MET cc_start: 0.7915 (ptp) cc_final: 0.7568 (ptp) REVERT: E 211 GLU cc_start: 0.7929 (tt0) cc_final: 0.7128 (pt0) REVERT: E 333 ILE cc_start: 0.8810 (mt) cc_final: 0.8529 (tt) REVERT: E 375 SER cc_start: 0.9046 (t) cc_final: 0.8743 (m) REVERT: E 475 MET cc_start: 0.7853 (tpp) cc_final: 0.7563 (tpp) REVERT: J 2 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7918 (m) REVERT: J 81 GLN cc_start: 0.8153 (tp40) cc_final: 0.7492 (tp40) REVERT: M 79 GLN cc_start: 0.6660 (pt0) cc_final: 0.6344 (pp30) REVERT: O 39 GLN cc_start: 0.7214 (pt0) cc_final: 0.6758 (pp30) REVERT: O 81 LYS cc_start: 0.7712 (ttmm) cc_final: 0.6530 (ttpp) REVERT: O 100 ASP cc_start: 0.8159 (t0) cc_final: 0.7957 (m-30) REVERT: O 102 PHE cc_start: 0.8442 (m-80) cc_final: 0.8019 (m-10) REVERT: Q 36 TYR cc_start: 0.7908 (m-80) cc_final: 0.7570 (m-80) REVERT: Q 69 THR cc_start: 0.8389 (p) cc_final: 0.7938 (t) REVERT: Q 103 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.6867 (tpm170) REVERT: F 97 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8767 (mmtm) REVERT: F 106 GLU cc_start: 0.8190 (tt0) cc_final: 0.7976 (tt0) REVERT: F 117 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8308 (tptt) REVERT: F 370 GLU cc_start: 0.7788 (tt0) cc_final: 0.7392 (mp0) REVERT: F 440 GLN cc_start: 0.8104 (tp40) cc_final: 0.7790 (tp-100) REVERT: K 81 GLN cc_start: 0.8145 (tp40) cc_final: 0.7477 (tp40) REVERT: N 79 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6072 (pp30) REVERT: N 103 ARG cc_start: 0.8639 (tpt170) cc_final: 0.7706 (mmp-170) REVERT: P 39 GLN cc_start: 0.7300 (pp30) cc_final: 0.6672 (pp30) REVERT: P 60 ASN cc_start: 0.8005 (t0) cc_final: 0.7350 (t0) REVERT: P 66 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6771 (mtm110) REVERT: P 81 LYS cc_start: 0.7975 (tttt) cc_final: 0.7703 (ttpp) REVERT: P 100 GLU cc_start: 0.8842 (pm20) cc_final: 0.8316 (pm20) REVERT: P 102 PHE cc_start: 0.8388 (m-80) cc_final: 0.8167 (m-80) REVERT: R 69 THR cc_start: 0.8549 (p) cc_final: 0.8092 (t) REVERT: R 89 GLN cc_start: 0.6809 (mt0) cc_final: 0.6547 (tt0) REVERT: R 102 THR cc_start: 0.5367 (p) cc_final: 0.4913 (p) outliers start: 85 outliers final: 62 residues processed: 518 average time/residue: 0.3463 time to fit residues: 285.3963 Evaluate side-chains 521 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 455 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 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 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 45 LYS Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 87 THR 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 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 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 G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain F residue 111 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 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 45 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN 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 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 229 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 137 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 27BASN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111723 restraints weight = 36880.086| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.71 r_work: 0.3258 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24990 Z= 0.126 Angle : 0.586 13.319 34026 Z= 0.295 Chirality : 0.043 0.181 3903 Planarity : 0.004 0.043 4236 Dihedral : 4.972 37.470 4446 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.06 % Allowed : 13.65 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2973 helix: 1.94 (0.27), residues: 417 sheet: 0.72 (0.18), residues: 867 loop : -0.04 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 36 HIS 0.006 0.001 HIS K 82A PHE 0.015 0.001 PHE O 78 TYR 0.017 0.001 TYR J 91 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 45) link_NAG-ASN : angle 1.95720 ( 135) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 1.28605 ( 36) hydrogen bonds : bond 0.03526 ( 693) hydrogen bonds : angle 4.87302 ( 1755) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.98669 ( 84) covalent geometry : bond 0.00300 (24891) covalent geometry : angle 0.56480 (33771) *********************** 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 550 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 470 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9119 (m) cc_final: 0.8819 (p) REVERT: A 82 GLN cc_start: 0.8353 (mp10) cc_final: 0.7995 (mp10) REVERT: A 97 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8696 (mmtm) REVERT: A 141 MET cc_start: 0.7789 (ptp) cc_final: 0.7425 (ptp) REVERT: A 166 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7350 (ttp-110) REVERT: A 211 GLU cc_start: 0.8082 (tt0) cc_final: 0.7399 (pt0) REVERT: A 217 TYR cc_start: 0.8641 (m-80) cc_final: 0.8023 (m-80) REVERT: A 308 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8485 (mtp-110) REVERT: A 328 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7961 (ttm) REVERT: A 492 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7991 (mt-10) REVERT: D 69 ASN cc_start: 0.8942 (m-40) cc_final: 0.8461 (m110) REVERT: D 91 TYR cc_start: 0.9173 (t80) cc_final: 0.8672 (t80) REVERT: B 634 GLU cc_start: 0.7485 (tt0) cc_final: 0.7174 (tt0) REVERT: H 60 ASN cc_start: 0.8038 (t0) cc_final: 0.7729 (t0) REVERT: H 66 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6731 (mtm110) REVERT: H 90 TYR cc_start: 0.7417 (m-10) cc_final: 0.7194 (m-10) REVERT: L 53 LYS cc_start: 0.8297 (mttm) cc_final: 0.8032 (mtmm) REVERT: L 69 THR cc_start: 0.8538 (p) cc_final: 0.8152 (t) REVERT: L 89 GLN cc_start: 0.6848 (mt0) cc_final: 0.6584 (tt0) REVERT: E 51 THR cc_start: 0.9366 (m) cc_final: 0.9010 (p) REVERT: E 97 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8624 (mmtm) REVERT: E 117 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8232 (tptt) REVERT: E 141 MET cc_start: 0.8023 (ptp) cc_final: 0.7652 (ptp) REVERT: E 211 GLU cc_start: 0.7887 (tt0) cc_final: 0.7096 (pt0) REVERT: E 333 ILE cc_start: 0.8803 (mt) cc_final: 0.8518 (tt) REVERT: E 375 SER cc_start: 0.9058 (t) cc_final: 0.8758 (m) REVERT: E 475 MET cc_start: 0.7922 (tpp) cc_final: 0.7546 (tpp) REVERT: J 2 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7825 (m) REVERT: J 81 GLN cc_start: 0.8151 (tp40) cc_final: 0.7459 (tp40) REVERT: M 45 LYS cc_start: 0.8032 (tttt) cc_final: 0.7696 (ptmm) REVERT: O 39 GLN cc_start: 0.7111 (pt0) cc_final: 0.6762 (pp30) REVERT: O 81 LYS cc_start: 0.7705 (ttmm) cc_final: 0.6492 (ttpp) REVERT: O 100 GLU cc_start: 0.8698 (pm20) cc_final: 0.8223 (pm20) REVERT: O 102 PHE cc_start: 0.8447 (m-80) cc_final: 0.8009 (m-10) REVERT: Q 36 TYR cc_start: 0.7880 (m-80) cc_final: 0.7481 (m-80) REVERT: Q 69 THR cc_start: 0.8376 (p) cc_final: 0.7946 (t) REVERT: Q 103 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.6845 (tpm170) REVERT: F 97 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8769 (mmtm) REVERT: F 117 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8297 (tptt) REVERT: F 370 GLU cc_start: 0.7733 (tt0) cc_final: 0.7387 (mp0) REVERT: K 81 GLN cc_start: 0.8255 (tp40) cc_final: 0.7387 (tp40) REVERT: N 79 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: N 103 ARG cc_start: 0.8627 (tpt170) cc_final: 0.7697 (mmp-170) REVERT: P 39 GLN cc_start: 0.7321 (pp30) cc_final: 0.6926 (pp30) REVERT: P 60 ASN cc_start: 0.7993 (t0) cc_final: 0.7346 (t0) REVERT: P 100 GLU cc_start: 0.8733 (pm20) cc_final: 0.8161 (pm20) REVERT: R 35 TRP cc_start: 0.7206 (m100) cc_final: 0.6887 (m100) REVERT: R 69 THR cc_start: 0.8535 (p) cc_final: 0.8095 (t) REVERT: R 89 GLN cc_start: 0.6803 (mt0) cc_final: 0.6601 (tt0) REVERT: R 102 THR cc_start: 0.5474 (p) cc_final: 0.5016 (p) outliers start: 80 outliers final: 67 residues processed: 517 average time/residue: 0.3350 time to fit residues: 276.4314 Evaluate side-chains 527 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 457 time to evaluate : 2.662 ------------------------------------------------------------------------------- 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 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 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 63 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 SER 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 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 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 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 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 G residue 625 ASN Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain F residue 111 LEU 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 295 ASN 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 110 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN 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 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 28 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 123 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN D 79 GLN M 79 GLN N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114454 restraints weight = 37316.572| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.72 r_work: 0.3254 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24990 Z= 0.125 Angle : 0.583 12.782 34026 Z= 0.294 Chirality : 0.043 0.181 3903 Planarity : 0.004 0.046 4236 Dihedral : 4.930 37.939 4446 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 13.95 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 2973 helix: 1.97 (0.27), residues: 417 sheet: 0.72 (0.18), residues: 867 loop : -0.04 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 36 HIS 0.004 0.001 HIS E 330 PHE 0.022 0.001 PHE F 53 TYR 0.017 0.001 TYR J 91 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 45) link_NAG-ASN : angle 1.93587 ( 135) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.23299 ( 36) hydrogen bonds : bond 0.03520 ( 693) hydrogen bonds : angle 4.89392 ( 1755) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.99215 ( 84) covalent geometry : bond 0.00301 (24891) covalent geometry : angle 0.56198 (33771) *********************** 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 556 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 468 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9115 (m) cc_final: 0.8872 (p) REVERT: A 82 GLN cc_start: 0.8244 (mp10) cc_final: 0.7900 (mp10) REVERT: A 97 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8624 (mmtm) REVERT: A 141 MET cc_start: 0.7536 (ptp) cc_final: 0.7165 (ptp) REVERT: A 166 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7314 (ttp-110) REVERT: A 211 GLU cc_start: 0.7981 (tt0) cc_final: 0.7246 (pt0) REVERT: A 217 TYR cc_start: 0.8485 (m-80) cc_final: 0.8098 (m-80) REVERT: A 328 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7856 (ttm) REVERT: A 492 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 23 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.7873 (tpp-160) REVERT: D 69 ASN cc_start: 0.8898 (m-40) cc_final: 0.8448 (m110) REVERT: D 79 GLN cc_start: 0.7020 (pt0) cc_final: 0.6414 (pp30) REVERT: D 82 ASP cc_start: 0.6499 (m-30) cc_final: 0.5906 (m-30) REVERT: D 91 TYR cc_start: 0.9099 (t80) cc_final: 0.8617 (t80) REVERT: B 634 GLU cc_start: 0.7174 (tt0) cc_final: 0.6892 (tt0) REVERT: H 60 ASN cc_start: 0.8008 (t0) cc_final: 0.7704 (t0) REVERT: H 66 ARG cc_start: 0.7232 (mtm180) cc_final: 0.6844 (mtm110) REVERT: L 53 LYS cc_start: 0.8300 (mttm) cc_final: 0.8043 (mtmm) REVERT: L 69 THR cc_start: 0.8479 (p) cc_final: 0.8114 (t) REVERT: L 89 GLN cc_start: 0.6786 (mt0) cc_final: 0.6560 (tt0) REVERT: E 51 THR cc_start: 0.9343 (m) cc_final: 0.9019 (p) REVERT: E 97 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8545 (mmtm) REVERT: E 117 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8209 (tptt) REVERT: E 211 GLU cc_start: 0.7942 (tt0) cc_final: 0.7149 (pt0) REVERT: E 328 MET cc_start: 0.8410 (ttm) cc_final: 0.7761 (ttp) REVERT: E 333 ILE cc_start: 0.8664 (mt) cc_final: 0.8433 (tt) REVERT: E 375 SER cc_start: 0.8930 (t) cc_final: 0.8653 (m) REVERT: E 440 GLN cc_start: 0.8071 (tp40) cc_final: 0.7458 (tp-100) REVERT: J 2 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7804 (m) REVERT: J 81 GLN cc_start: 0.8070 (tp40) cc_final: 0.7408 (tp40) REVERT: M 79 GLN cc_start: 0.6766 (pt0) cc_final: 0.6420 (pp30) REVERT: O 81 LYS cc_start: 0.7638 (ttmm) cc_final: 0.6438 (ttpp) REVERT: O 100 GLU cc_start: 0.8597 (pm20) cc_final: 0.8113 (pm20) REVERT: O 102 PHE cc_start: 0.8331 (m-80) cc_final: 0.7867 (m-10) REVERT: Q 36 TYR cc_start: 0.7741 (m-80) cc_final: 0.7354 (m-80) REVERT: Q 69 THR cc_start: 0.8292 (p) cc_final: 0.7883 (t) REVERT: Q 103 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.6893 (tpm170) REVERT: F 97 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8679 (mmtm) REVERT: F 106 GLU cc_start: 0.7954 (tt0) cc_final: 0.7587 (tt0) REVERT: F 117 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8261 (tptt) REVERT: F 370 GLU cc_start: 0.7539 (tt0) cc_final: 0.7335 (mp0) REVERT: F 440 GLN cc_start: 0.7900 (tp40) cc_final: 0.7497 (tp-100) REVERT: K 81 GLN cc_start: 0.8327 (tp40) cc_final: 0.7513 (tp40) REVERT: K 82 MET cc_start: 0.7984 (mmm) cc_final: 0.7767 (mmm) REVERT: N 103 ARG cc_start: 0.8673 (tpt170) cc_final: 0.7791 (mmp-170) REVERT: I 638 TYR cc_start: 0.8698 (m-80) cc_final: 0.8476 (m-80) REVERT: P 60 ASN cc_start: 0.7969 (t0) cc_final: 0.7320 (t0) REVERT: P 100 GLU cc_start: 0.8667 (pm20) cc_final: 0.8032 (pm20) REVERT: R 35 TRP cc_start: 0.7100 (m100) cc_final: 0.6762 (m100) REVERT: R 69 THR cc_start: 0.8495 (p) cc_final: 0.8066 (t) REVERT: R 102 THR cc_start: 0.5443 (p) cc_final: 0.4996 (p) outliers start: 88 outliers final: 72 residues processed: 515 average time/residue: 0.3386 time to fit residues: 280.7562 Evaluate side-chains 534 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 460 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 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 5 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 SER 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 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 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 303 THR 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 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 100 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 111 LEU 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 295 ASN 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 F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 110 THR 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 20 LEU Chi-restraints excluded: chain P residue 82 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 141 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 241 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 HIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS ** N 37 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111324 restraints weight = 37407.951| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.70 r_work: 0.3223 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3872 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= 0.170 Angle : 0.614 12.829 34026 Z= 0.310 Chirality : 0.044 0.213 3903 Planarity : 0.004 0.048 4236 Dihedral : 5.090 39.706 4446 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.02 % Allowed : 14.41 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2973 helix: 1.86 (0.27), residues: 417 sheet: 0.58 (0.17), residues: 900 loop : -0.11 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 36 HIS 0.004 0.001 HIS E 330 PHE 0.014 0.002 PHE C 67 TYR 0.019 0.001 TYR M 91 ARG 0.005 0.000 ARG Q 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 45) link_NAG-ASN : angle 2.01342 ( 135) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.22728 ( 36) hydrogen bonds : bond 0.03771 ( 693) hydrogen bonds : angle 5.01737 ( 1755) SS BOND : bond 0.00449 ( 42) SS BOND : angle 2.17593 ( 84) covalent geometry : bond 0.00410 (24891) covalent geometry : angle 0.59142 (33771) *********************** 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 538 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 459 time to evaluate : 2.853 Fit side-chains REVERT: A 51 THR cc_start: 0.9191 (m) cc_final: 0.8972 (p) REVERT: A 82 GLN cc_start: 0.8358 (mp10) cc_final: 0.7983 (mp10) REVERT: A 97 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8750 (mmtm) REVERT: A 141 MET cc_start: 0.7760 (ptp) cc_final: 0.7365 (ptp) REVERT: A 211 GLU cc_start: 0.8094 (tt0) cc_final: 0.7380 (pt0) REVERT: A 217 TYR cc_start: 0.8658 (m-80) cc_final: 0.8063 (m-80) REVERT: A 328 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8046 (ttm) REVERT: C 27 TYR cc_start: 0.8051 (p90) cc_final: 0.7765 (p90) REVERT: D 69 ASN cc_start: 0.8950 (m-40) cc_final: 0.8434 (m110) REVERT: H 39 GLN cc_start: 0.7098 (pp30) cc_final: 0.6683 (pp30) REVERT: H 60 ASN cc_start: 0.8036 (t0) cc_final: 0.7783 (t0) REVERT: H 66 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6887 (mtm110) REVERT: L 53 LYS cc_start: 0.8477 (mttm) cc_final: 0.8157 (mtmm) REVERT: L 69 THR cc_start: 0.8544 (p) cc_final: 0.8165 (t) REVERT: E 51 THR cc_start: 0.9385 (m) cc_final: 0.9055 (p) REVERT: E 97 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8667 (mmtm) REVERT: E 106 GLU cc_start: 0.8363 (tt0) cc_final: 0.8099 (tt0) REVERT: E 117 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8285 (tptt) REVERT: E 141 MET cc_start: 0.7782 (ptp) cc_final: 0.7546 (ptp) REVERT: E 211 GLU cc_start: 0.8041 (tt0) cc_final: 0.7250 (pt0) REVERT: E 328 MET cc_start: 0.8407 (ttm) cc_final: 0.7879 (ttm) REVERT: E 333 ILE cc_start: 0.8766 (mt) cc_final: 0.8497 (tt) REVERT: E 375 SER cc_start: 0.9092 (t) cc_final: 0.8802 (m) REVERT: E 475 MET cc_start: 0.7862 (tpp) cc_final: 0.7590 (tpp) REVERT: J 2 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7854 (m) REVERT: J 81 GLN cc_start: 0.8097 (tp40) cc_final: 0.7386 (tp40) REVERT: O 81 LYS cc_start: 0.7714 (ttmm) cc_final: 0.6536 (ttpp) REVERT: O 100 GLU cc_start: 0.8725 (pm20) cc_final: 0.8320 (pm20) REVERT: Q 69 THR cc_start: 0.8379 (p) cc_final: 0.7929 (t) REVERT: Q 103 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.6899 (tpm170) REVERT: F 97 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8774 (mmtm) REVERT: F 117 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8297 (tptt) REVERT: F 141 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6454 (tpp) REVERT: F 328 MET cc_start: 0.8352 (ttm) cc_final: 0.7927 (ttp) REVERT: F 370 GLU cc_start: 0.7817 (tt0) cc_final: 0.7442 (mp0) REVERT: F 475 MET cc_start: 0.8187 (mmm) cc_final: 0.7979 (tpp) REVERT: K 81 GLN cc_start: 0.8470 (tp40) cc_final: 0.7621 (tp40) REVERT: N 103 ARG cc_start: 0.8720 (tpt170) cc_final: 0.7821 (mmp-170) REVERT: I 638 TYR cc_start: 0.8836 (m-80) cc_final: 0.8563 (m-80) REVERT: P 60 ASN cc_start: 0.8002 (t0) cc_final: 0.7360 (t0) REVERT: P 100 GLU cc_start: 0.8752 (pm20) cc_final: 0.8459 (pm20) REVERT: P 100 GLU cc_start: 0.7824 (mp0) cc_final: 0.7596 (mp0) REVERT: R 69 THR cc_start: 0.8548 (p) cc_final: 0.8096 (t) REVERT: R 102 THR cc_start: 0.5445 (p) cc_final: 0.4985 (p) outliers start: 79 outliers final: 69 residues processed: 504 average time/residue: 0.3516 time to fit residues: 283.7525 Evaluate side-chains 526 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 454 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 292 VAL 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 5 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 SER 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 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 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 426 MET Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL 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 70 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 MET 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 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 F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 100 ASP 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 259 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113654 restraints weight = 37336.020| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.74 r_work: 0.3240 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24990 Z= 0.137 Angle : 0.612 17.368 34026 Z= 0.309 Chirality : 0.044 0.361 3903 Planarity : 0.004 0.050 4236 Dihedral : 5.097 39.400 4446 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.87 % Allowed : 14.87 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 2973 helix: 1.93 (0.27), residues: 417 sheet: 0.58 (0.17), residues: 900 loop : -0.10 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 36 HIS 0.009 0.001 HIS E 330 PHE 0.021 0.001 PHE F 53 TYR 0.017 0.001 TYR J 91 ARG 0.005 0.000 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 45) link_NAG-ASN : angle 2.02992 ( 135) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.17033 ( 36) hydrogen bonds : bond 0.03593 ( 693) hydrogen bonds : angle 4.94651 ( 1755) SS BOND : bond 0.00481 ( 42) SS BOND : angle 2.41801 ( 84) covalent geometry : bond 0.00327 (24891) covalent geometry : angle 0.58729 (33771) ********************** 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 537 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 462 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8342 (mp10) cc_final: 0.7959 (mp10) REVERT: A 97 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8750 (mmtm) REVERT: A 141 MET cc_start: 0.7814 (ptp) cc_final: 0.7470 (ptp) REVERT: A 211 GLU cc_start: 0.8088 (tt0) cc_final: 0.7363 (pt0) REVERT: A 217 TYR cc_start: 0.8611 (m-80) cc_final: 0.8331 (m-80) REVERT: A 328 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8045 (ttm) REVERT: A 492 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8042 (mt-10) REVERT: C 23 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.7866 (tpp-160) REVERT: C 27 TYR cc_start: 0.8106 (p90) cc_final: 0.7825 (p90) REVERT: D 69 ASN cc_start: 0.8897 (m-40) cc_final: 0.8367 (m110) REVERT: D 79 GLN cc_start: 0.6868 (pt0) cc_final: 0.6244 (pp30) REVERT: H 60 ASN cc_start: 0.7991 (t0) cc_final: 0.7751 (t0) REVERT: H 66 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6890 (mtm110) REVERT: L 53 LYS cc_start: 0.8468 (mttm) cc_final: 0.8179 (mtmm) REVERT: L 69 THR cc_start: 0.8532 (p) cc_final: 0.8153 (t) REVERT: L 89 GLN cc_start: 0.7142 (tt0) cc_final: 0.6896 (tt0) REVERT: L 102 THR cc_start: 0.5143 (p) cc_final: 0.4693 (p) REVERT: E 51 THR cc_start: 0.9394 (m) cc_final: 0.9080 (p) REVERT: E 97 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8658 (mmtm) REVERT: E 106 GLU cc_start: 0.8351 (tt0) cc_final: 0.8077 (tt0) REVERT: E 117 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8279 (tptt) REVERT: E 141 MET cc_start: 0.7692 (ptp) cc_final: 0.7317 (ptp) REVERT: E 211 GLU cc_start: 0.8009 (tt0) cc_final: 0.7241 (pt0) REVERT: E 328 MET cc_start: 0.8425 (ttm) cc_final: 0.7569 (ttp) REVERT: E 333 ILE cc_start: 0.8859 (mt) cc_final: 0.8535 (tt) REVERT: E 375 SER cc_start: 0.9049 (t) cc_final: 0.8740 (m) REVERT: E 475 MET cc_start: 0.7826 (tpp) cc_final: 0.7485 (tpp) REVERT: J 2 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7835 (m) REVERT: J 81 GLN cc_start: 0.8096 (tp40) cc_final: 0.7391 (tp40) REVERT: M 79 GLN cc_start: 0.6657 (pt0) cc_final: 0.6320 (pp30) REVERT: O 81 LYS cc_start: 0.7674 (ttmm) cc_final: 0.6482 (ttpp) REVERT: O 100 GLU cc_start: 0.8715 (pm20) cc_final: 0.8314 (pm20) REVERT: Q 36 TYR cc_start: 0.7915 (m-80) cc_final: 0.7407 (m-80) REVERT: Q 69 THR cc_start: 0.8344 (p) cc_final: 0.7888 (t) REVERT: Q 103 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.6893 (tpm170) REVERT: F 97 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8725 (mmtm) REVERT: F 106 GLU cc_start: 0.8207 (tt0) cc_final: 0.7865 (tt0) REVERT: F 117 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8290 (tptt) REVERT: F 328 MET cc_start: 0.8388 (ttm) cc_final: 0.7920 (ttp) REVERT: F 370 GLU cc_start: 0.7838 (tt0) cc_final: 0.7421 (mp0) REVERT: F 440 GLN cc_start: 0.8238 (tp40) cc_final: 0.7873 (tp-100) REVERT: F 475 MET cc_start: 0.8142 (mmm) cc_final: 0.7920 (tpp) REVERT: K 81 GLN cc_start: 0.8536 (tp40) cc_final: 0.7717 (tp40) REVERT: K 100 TYR cc_start: 0.9009 (m-80) cc_final: 0.8764 (m-80) REVERT: N 45 LYS cc_start: 0.8177 (pttp) cc_final: 0.7817 (ptmm) REVERT: N 103 ARG cc_start: 0.8717 (tpt170) cc_final: 0.7819 (mmp-170) REVERT: I 638 TYR cc_start: 0.8827 (m-80) cc_final: 0.8560 (m-80) REVERT: P 60 ASN cc_start: 0.7944 (t0) cc_final: 0.7311 (t0) REVERT: P 100 GLU cc_start: 0.8684 (pm20) cc_final: 0.8173 (pm20) REVERT: P 100 GLU cc_start: 0.7831 (mp0) cc_final: 0.7623 (mp0) REVERT: R 69 THR cc_start: 0.8538 (p) cc_final: 0.8078 (t) REVERT: R 102 THR cc_start: 0.5407 (p) cc_final: 0.4940 (p) outliers start: 75 outliers final: 65 residues processed: 506 average time/residue: 0.3418 time to fit residues: 276.8600 Evaluate side-chains 525 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 458 time to evaluate : 2.521 ------------------------------------------------------------------------------- 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 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 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 5 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 65 SER 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 96 GLN 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 426 MET Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain J residue 2 VAL 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 100 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain F residue 111 LEU 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 295 ASN 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 F residue 488 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 63 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 82 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain R residue 10 SER 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 235 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** C 39 GLN C 82AHIS ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** F 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108653 restraints weight = 36713.636| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.70 r_work: 0.3211 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24990 Z= 0.193 Angle : 0.670 19.799 34026 Z= 0.337 Chirality : 0.046 0.356 3903 Planarity : 0.004 0.050 4236 Dihedral : 5.293 40.141 4446 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 14.95 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 2973 helix: 1.78 (0.27), residues: 417 sheet: 0.52 (0.18), residues: 900 loop : -0.14 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 36 HIS 0.005 0.001 HIS A 330 PHE 0.011 0.002 PHE O 78 TYR 0.020 0.001 TYR M 91 ARG 0.008 0.001 ARG P 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 45) link_NAG-ASN : angle 2.26553 ( 135) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.19461 ( 36) hydrogen bonds : bond 0.03824 ( 693) hydrogen bonds : angle 5.02425 ( 1755) SS BOND : bond 0.00595 ( 42) SS BOND : angle 2.90832 ( 84) covalent geometry : bond 0.00464 (24891) covalent geometry : angle 0.63924 (33771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14299.99 seconds wall clock time: 248 minutes 29.00 seconds (14909.00 seconds total)