Starting phenix.real_space_refine on Fri May 23 18:33:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4d_41027/05_2025/8t4d_41027.cif" } resolution = 3.1 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= 0.027 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 159 5.16 5 C 15567 2.51 5 N 4167 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24753 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} Chain: "E" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "Q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} Chain: "F" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "R" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 98} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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: 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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: 15.55, per 1000 atoms: 0.63 Number of scatterers: 24753 At special positions: 0 Unit cell: (156.6, 152.424, 173.304, 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 159 16.00 O 4860 8.00 N 4167 7.00 C 15567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 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=2.03 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 A 501 " - pdb=" SG CYS B 605 " distance=2.02 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=2.04 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 H 99 " - pdb=" SG CYS H 100D" 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=2.03 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=2.03 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 E 501 " - pdb=" SG CYS G 605 " distance=2.02 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=2.04 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 O 99 " - pdb=" SG CYS O 100D" 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=2.03 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 F 501 " - pdb=" SG CYS I 605 " distance=2.02 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=2.04 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 P 99 " - pdb=" SG CYS P 100D" 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 U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " 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 339 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " 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 339 " " NAG E 609 " - " ASN E 386 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " 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 339 " " NAG F 609 " - " ASN F 386 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG G 701 " - " ASN G 611 " " NAG I 701 " - " ASN I 611 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 262 " Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.1 seconds 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5598 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 17.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.837A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.523A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.182A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.838A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.524A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.183A pdb=" N HIS O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.320A 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 335 through 354 removed outlier: 3.838A 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 474 through 484 removed outlier: 4.117A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.599A pdb=" N THR K 87 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.524A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.813A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.159A 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 624 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.183A pdb=" N HIS P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.597A pdb=" N VAL R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.081A 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 removed outlier: 3.693A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.532A 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: 6.780A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 315 " --> 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: 5.644A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (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: 6.337A 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 95A through 98 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'H' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100M through 103 Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR L 30 " --> pdb=" O ASP L 27D" (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.544A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 6.780A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN E 315 " --> 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=AC6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.645A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (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=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.337A 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 95A through 98 Processing sheet with id=AD1, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'O' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 9 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100M through 103 Processing sheet with id=AD3, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AD4, first strand: chain 'Q' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR Q 30 " --> pdb=" O ASP Q 27D" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 53 through 54 removed outlier: 6.543A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.229A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.693A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.794A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'F' and resid 200 through 203 removed outlier: 5.892A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, 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: 6.780A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN F 315 " --> 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=AE4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.644A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (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=AE6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.336A 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 95A through 98 Processing sheet with id=AE8, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'P' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 9 through 12 current: chain 'P' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100M through 103 Processing sheet with id=AF1, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'R' and resid 27C through 27D removed outlier: 3.717A pdb=" N THR R 30 " --> pdb=" O ASP R 27D" (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.544A pdb=" N ASN R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1872 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: 10.86 Time building geometry restraints manager: 7.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7814 1.34 - 1.47: 6439 1.47 - 1.59: 10806 1.59 - 1.71: 0 1.71 - 1.84: 222 Bond restraints: 25281 Sorted by residual: bond pdb=" N SER F 140 " pdb=" CA SER F 140 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.61e+01 bond pdb=" N SER A 140 " pdb=" CA SER A 140 " ideal model delta sigma weight residual 1.459 1.496 -0.036 9.10e-03 1.21e+04 1.61e+01 bond pdb=" N SER E 140 " pdb=" CA SER E 140 " ideal model delta sigma weight residual 1.459 1.496 -0.036 9.10e-03 1.21e+04 1.60e+01 bond pdb=" CB CYS J 92 " pdb=" SG CYS J 92 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.79e+00 bond pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.71e+00 ... (remaining 25276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 31632 1.79 - 3.58: 2273 3.58 - 5.38: 329 5.38 - 7.17: 47 7.17 - 8.96: 6 Bond angle restraints: 34287 Sorted by residual: angle pdb=" N GLY D 100 " pdb=" CA GLY D 100 " pdb=" C GLY D 100 " ideal model delta sigma weight residual 112.85 106.41 6.44 1.61e+00 3.86e-01 1.60e+01 angle pdb=" N GLY N 100 " pdb=" CA GLY N 100 " pdb=" C GLY N 100 " ideal model delta sigma weight residual 112.85 106.42 6.43 1.61e+00 3.86e-01 1.59e+01 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 106.43 6.42 1.61e+00 3.86e-01 1.59e+01 angle pdb=" N THR P 100 " pdb=" CA THR P 100 " pdb=" C THR P 100 " ideal model delta sigma weight residual 108.76 102.95 5.81 1.58e+00 4.01e-01 1.35e+01 angle pdb=" N THR O 100 " pdb=" CA THR O 100 " pdb=" C THR O 100 " ideal model delta sigma weight residual 108.76 102.96 5.80 1.58e+00 4.01e-01 1.35e+01 ... (remaining 34282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 15330 21.14 - 42.28: 367 42.28 - 63.42: 119 63.42 - 84.56: 39 84.56 - 105.70: 18 Dihedral angle restraints: 15873 sinusoidal: 7119 harmonic: 8754 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.73 -41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " pdb=" CB CYS J 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.72 -41.72 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.70 -41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 15870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2817 0.061 - 0.122: 968 0.122 - 0.183: 159 0.183 - 0.244: 13 0.244 - 0.305: 6 Chirality restraints: 3963 Sorted by residual: chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 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 ... (remaining 3960 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 480 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ARG F 480 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG F 480 " -0.024 2.00e-02 2.50e+03 pdb=" N SER F 481 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 480 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG E 480 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG E 480 " -0.024 2.00e-02 2.50e+03 pdb=" N SER E 481 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 480 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG A 480 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG A 480 " 0.024 2.00e-02 2.50e+03 pdb=" N SER A 481 " 0.022 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 158 2.58 - 3.16: 19636 3.16 - 3.74: 37292 3.74 - 4.32: 55255 4.32 - 4.90: 90546 Nonbonded interactions: 202887 Sorted by model distance: nonbonded pdb=" NH1 ARG E 151 " pdb=" OE2 GLU O 97 " model vdw 2.005 3.120 nonbonded pdb=" NH1 ARG A 151 " pdb=" OE2 GLU H 97 " model vdw 2.071 3.120 nonbonded pdb=" NH1 ARG F 151 " pdb=" OE2 GLU P 97 " model vdw 2.073 3.120 nonbonded pdb=" O GLY C 96 " pdb=" OH TYR D 96 " model vdw 2.162 3.040 nonbonded pdb=" O GLY K 96 " pdb=" OH TYR N 96 " model vdw 2.162 3.040 ... (remaining 202882 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: 0.16 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 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'a' } 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: 6.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 59.870 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 0.072 25392 Z= 0.279 Angle : 1.030 8.962 34572 Z= 0.580 Chirality : 0.059 0.305 3963 Planarity : 0.005 0.038 4299 Dihedral : 11.136 105.699 10131 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.23 % Allowed : 0.57 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.96 (0.14), residues: 2994 helix: 0.53 (0.25), residues: 429 sheet: 1.24 (0.16), residues: 948 loop : 0.41 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 614 HIS 0.006 0.002 HIS F 374 PHE 0.024 0.003 PHE P 100B TYR 0.023 0.003 TYR O 98 ARG 0.014 0.001 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 51) link_NAG-ASN : angle 2.82342 ( 153) link_BETA1-4 : bond 0.00377 ( 12) link_BETA1-4 : angle 1.28251 ( 36) hydrogen bonds : bond 0.13115 ( 723) hydrogen bonds : angle 6.36432 ( 1872) SS BOND : bond 0.00701 ( 48) SS BOND : angle 1.93770 ( 96) covalent geometry : bond 0.00611 (25281) covalent geometry : angle 1.01112 (34287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 600 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7718 (mtm110) REVERT: D 47 MET cc_start: 0.8575 (mmm) cc_final: 0.8304 (mmp) REVERT: D 52 THR cc_start: 0.8510 (p) cc_final: 0.8202 (m) REVERT: D 66 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8056 (tttt) REVERT: B 575 GLN cc_start: 0.7721 (mt0) cc_final: 0.7454 (tt0) REVERT: B 652 GLN cc_start: 0.8642 (mt0) cc_final: 0.8414 (mt0) REVERT: B 653 GLN cc_start: 0.8340 (tt0) cc_final: 0.7540 (mt0) REVERT: E 110 SER cc_start: 0.8511 (t) cc_final: 0.8274 (m) REVERT: E 166 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7710 (mtm110) REVERT: E 198 THR cc_start: 0.8800 (m) cc_final: 0.8474 (m) REVERT: M 52 THR cc_start: 0.8462 (p) cc_final: 0.8174 (m) REVERT: F 110 SER cc_start: 0.8559 (t) cc_final: 0.8291 (m) REVERT: F 166 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7645 (mtm110) REVERT: F 198 THR cc_start: 0.8760 (m) cc_final: 0.8407 (m) REVERT: F 212 PRO cc_start: 0.8957 (Cg_exo) cc_final: 0.8601 (Cg_endo) REVERT: N 47 MET cc_start: 0.8517 (mmm) cc_final: 0.8284 (mmm) REVERT: N 52 THR cc_start: 0.8443 (p) cc_final: 0.8170 (m) outliers start: 6 outliers final: 4 residues processed: 606 average time/residue: 0.3920 time to fit residues: 364.1245 Evaluate side-chains 404 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 400 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain F residue 241 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 577 GLN B 630 GLN B 637 ASN H 39 GLN E 94 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN M 95 GLN O 39 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN N 95 GLN I 637 ASN P 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124187 restraints weight = 30308.034| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.46 r_work: 0.3292 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25392 Z= 0.178 Angle : 0.646 12.590 34572 Z= 0.330 Chirality : 0.049 0.563 3963 Planarity : 0.004 0.036 4299 Dihedral : 7.237 61.240 4618 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 5.86 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.40 (0.15), residues: 2994 helix: 1.94 (0.27), residues: 411 sheet: 1.38 (0.16), residues: 897 loop : 0.51 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 35 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.002 PHE C 29 TYR 0.023 0.002 TYR H 98 ARG 0.006 0.001 ARG F 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 51) link_NAG-ASN : angle 2.86787 ( 153) link_BETA1-4 : bond 0.00337 ( 12) link_BETA1-4 : angle 1.68538 ( 36) hydrogen bonds : bond 0.04429 ( 723) hydrogen bonds : angle 5.08548 ( 1872) SS BOND : bond 0.00563 ( 48) SS BOND : angle 1.21731 ( 96) covalent geometry : bond 0.00408 (25281) covalent geometry : angle 0.61345 (34287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 416 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8614 (tttm) cc_final: 0.8192 (mttm) REVERT: A 123 THR cc_start: 0.9128 (m) cc_final: 0.8853 (p) REVERT: A 166 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7811 (mtm110) REVERT: C 18 LEU cc_start: 0.8336 (tp) cc_final: 0.8050 (tp) REVERT: H 39 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: L 54 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7606 (ttm110) REVERT: E 110 SER cc_start: 0.8599 (t) cc_final: 0.8265 (m) REVERT: E 123 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8946 (p) REVERT: E 166 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7637 (ttp80) REVERT: J 66 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7760 (mtm110) REVERT: M 47 MET cc_start: 0.8769 (mmm) cc_final: 0.8526 (mmt) REVERT: M 52 THR cc_start: 0.8492 (p) cc_final: 0.8237 (m) REVERT: O 39 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: O 77 THR cc_start: 0.8659 (m) cc_final: 0.8309 (p) REVERT: O 105 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7660 (ptp90) REVERT: Q 28 ASP cc_start: 0.8625 (m-30) cc_final: 0.8403 (m-30) REVERT: Q 33 LEU cc_start: 0.8717 (tp) cc_final: 0.8482 (tp) REVERT: Q 54 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7363 (ttm110) REVERT: F 110 SER cc_start: 0.8628 (t) cc_final: 0.8256 (m) REVERT: F 166 ARG cc_start: 0.8456 (mtp85) cc_final: 0.7728 (mtm110) REVERT: F 199 SER cc_start: 0.8963 (p) cc_final: 0.8567 (p) REVERT: F 269 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7752 (pt0) REVERT: N 47 MET cc_start: 0.8714 (mmm) cc_final: 0.8298 (mmt) REVERT: I 624 ASP cc_start: 0.9008 (m-30) cc_final: 0.8757 (m-30) outliers start: 58 outliers final: 38 residues processed: 455 average time/residue: 0.3688 time to fit residues: 261.0089 Evaluate side-chains 404 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 543 ASN G 637 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123466 restraints weight = 30375.511| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.39 r_work: 0.3290 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25392 Z= 0.146 Angle : 0.574 11.404 34572 Z= 0.293 Chirality : 0.046 0.479 3963 Planarity : 0.004 0.044 4299 Dihedral : 5.923 52.783 4614 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.70 % Allowed : 7.45 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.41 (0.15), residues: 2994 helix: 2.07 (0.27), residues: 411 sheet: 1.37 (0.17), residues: 897 loop : 0.50 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 50 HIS 0.004 0.001 HIS E 105 PHE 0.015 0.002 PHE H 100B TYR 0.014 0.001 TYR J 27 ARG 0.005 0.000 ARG P 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 51) link_NAG-ASN : angle 2.57554 ( 153) link_BETA1-4 : bond 0.00413 ( 12) link_BETA1-4 : angle 1.44467 ( 36) hydrogen bonds : bond 0.03865 ( 723) hydrogen bonds : angle 4.74074 ( 1872) SS BOND : bond 0.00712 ( 48) SS BOND : angle 1.07646 ( 96) covalent geometry : bond 0.00339 (25281) covalent geometry : angle 0.54514 (34287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 399 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8593 (tttm) cc_final: 0.8236 (mttm) REVERT: A 123 THR cc_start: 0.9135 (m) cc_final: 0.8913 (p) REVERT: A 166 ARG cc_start: 0.8538 (mtp85) cc_final: 0.7687 (ttp80) REVERT: H 66 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6923 (ttp-170) REVERT: H 105 ARG cc_start: 0.7988 (ptp90) cc_final: 0.7684 (ptp90) REVERT: L 54 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7655 (ttm110) REVERT: E 110 SER cc_start: 0.8601 (t) cc_final: 0.8227 (m) REVERT: E 166 ARG cc_start: 0.8470 (mtp85) cc_final: 0.7665 (ttp80) REVERT: E 269 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7779 (pt0) REVERT: M 52 THR cc_start: 0.8568 (p) cc_final: 0.8305 (m) REVERT: O 77 THR cc_start: 0.8612 (m) cc_final: 0.8391 (p) REVERT: Q 28 ASP cc_start: 0.8615 (m-30) cc_final: 0.8031 (m-30) REVERT: Q 31 THR cc_start: 0.8383 (m) cc_final: 0.7824 (p) REVERT: Q 33 LEU cc_start: 0.8820 (tp) cc_final: 0.8557 (tp) REVERT: Q 54 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7539 (ttm110) REVERT: F 110 SER cc_start: 0.8605 (t) cc_final: 0.8251 (m) REVERT: F 166 ARG cc_start: 0.8493 (mtp85) cc_final: 0.7613 (ttp80) REVERT: F 199 SER cc_start: 0.9087 (p) cc_final: 0.8706 (p) REVERT: F 269 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7697 (pt0) REVERT: N 47 MET cc_start: 0.8677 (mmm) cc_final: 0.8429 (mmt) REVERT: I 624 ASP cc_start: 0.9070 (m-30) cc_final: 0.8728 (m-30) REVERT: R 54 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7392 (ttm110) outliers start: 45 outliers final: 31 residues processed: 428 average time/residue: 0.3799 time to fit residues: 253.6393 Evaluate side-chains 394 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 137 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 228 optimal weight: 0.0020 chunk 278 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 271 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS C 39 GLN D 95 GLN H 39 GLN H 100KASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN O 39 GLN F 195 ASN N 95 GLN I 607 ASN P 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119412 restraints weight = 30451.100| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.25 r_work: 0.3259 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25392 Z= 0.118 Angle : 0.535 11.049 34572 Z= 0.271 Chirality : 0.045 0.430 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.376 52.607 4614 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 8.59 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.43 (0.16), residues: 2994 helix: 2.14 (0.26), residues: 411 sheet: 1.25 (0.17), residues: 933 loop : 0.57 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE J 67 TYR 0.012 0.001 TYR H 79 ARG 0.004 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 51) link_NAG-ASN : angle 2.48060 ( 153) link_BETA1-4 : bond 0.00386 ( 12) link_BETA1-4 : angle 1.35265 ( 36) hydrogen bonds : bond 0.03507 ( 723) hydrogen bonds : angle 4.56460 ( 1872) SS BOND : bond 0.00457 ( 48) SS BOND : angle 0.90840 ( 96) covalent geometry : bond 0.00270 (25281) covalent geometry : angle 0.50670 (34287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8641 (tttm) cc_final: 0.8170 (mttm) REVERT: A 123 THR cc_start: 0.9116 (m) cc_final: 0.8900 (p) REVERT: A 166 ARG cc_start: 0.8536 (mtp85) cc_final: 0.7918 (ptm-80) REVERT: C 82 MET cc_start: 0.8864 (ptp) cc_final: 0.8614 (mtm) REVERT: B 616 ASN cc_start: 0.8756 (p0) cc_final: 0.8481 (p0) REVERT: H 77 THR cc_start: 0.8680 (m) cc_final: 0.8349 (p) REVERT: L 28 ASP cc_start: 0.8754 (m-30) cc_final: 0.8339 (m-30) REVERT: L 54 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7695 (ttm110) REVERT: E 110 SER cc_start: 0.8593 (t) cc_final: 0.8204 (m) REVERT: E 166 ARG cc_start: 0.8579 (mtp85) cc_final: 0.7527 (ttp80) REVERT: Q 31 THR cc_start: 0.8410 (m) cc_final: 0.7852 (p) REVERT: Q 33 LEU cc_start: 0.8876 (tp) cc_final: 0.8587 (tp) REVERT: Q 54 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7497 (ttm110) REVERT: F 110 SER cc_start: 0.8589 (t) cc_final: 0.8229 (m) REVERT: F 166 ARG cc_start: 0.8511 (mtp85) cc_final: 0.7846 (mtm110) REVERT: F 269 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7720 (pt0) REVERT: N 47 MET cc_start: 0.8663 (mmm) cc_final: 0.8428 (mmt) REVERT: I 624 ASP cc_start: 0.9083 (m-30) cc_final: 0.8798 (m-30) REVERT: P 22 CYS cc_start: 0.7844 (t) cc_final: 0.7556 (t) REVERT: R 54 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7301 (ttm110) outliers start: 48 outliers final: 32 residues processed: 412 average time/residue: 0.3671 time to fit residues: 237.0287 Evaluate side-chains 388 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 0 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS D 95 GLN H 39 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS M 95 GLN O 39 GLN F 374 HIS N 95 GLN P 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118009 restraints weight = 30771.276| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.39 r_work: 0.3217 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25392 Z= 0.210 Angle : 0.600 11.285 34572 Z= 0.302 Chirality : 0.047 0.535 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.428 53.239 4614 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.23 % Allowed : 8.51 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.10 (0.16), residues: 2994 helix: 1.90 (0.26), residues: 411 sheet: 1.05 (0.17), residues: 915 loop : 0.35 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 96 HIS 0.004 0.001 HIS E 105 PHE 0.015 0.002 PHE F 383 TYR 0.013 0.002 TYR A 319 ARG 0.004 0.001 ARG K 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 51) link_NAG-ASN : angle 2.80372 ( 153) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.41976 ( 36) hydrogen bonds : bond 0.04079 ( 723) hydrogen bonds : angle 4.62223 ( 1872) SS BOND : bond 0.00503 ( 48) SS BOND : angle 1.14199 ( 96) covalent geometry : bond 0.00507 (25281) covalent geometry : angle 0.56762 (34287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 363 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8688 (tttm) cc_final: 0.8222 (mttm) REVERT: A 166 ARG cc_start: 0.8584 (mtp85) cc_final: 0.7737 (ttp80) REVERT: C 82 MET cc_start: 0.8856 (ptp) cc_final: 0.8599 (mtm) REVERT: B 616 ASN cc_start: 0.8723 (p0) cc_final: 0.8353 (p0) REVERT: H 66 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6824 (ttp-170) REVERT: L 28 ASP cc_start: 0.8824 (m-30) cc_final: 0.8437 (m-30) REVERT: L 54 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7705 (ttm110) REVERT: E 110 SER cc_start: 0.8638 (t) cc_final: 0.8202 (m) REVERT: E 166 ARG cc_start: 0.8622 (mtp85) cc_final: 0.7751 (ttp80) REVERT: O 39 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: Q 54 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7559 (ttm110) REVERT: F 110 SER cc_start: 0.8734 (t) cc_final: 0.8360 (m) REVERT: F 166 ARG cc_start: 0.8573 (mtp85) cc_final: 0.7875 (ttp80) REVERT: F 269 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7743 (pt0) REVERT: N 47 MET cc_start: 0.8686 (mmm) cc_final: 0.8455 (mmm) REVERT: I 544 LEU cc_start: 0.8716 (mt) cc_final: 0.8480 (mm) REVERT: I 616 ASN cc_start: 0.8821 (p0) cc_final: 0.8585 (p0) REVERT: I 624 ASP cc_start: 0.9070 (m-30) cc_final: 0.8781 (m-30) REVERT: P 66 ARG cc_start: 0.7066 (ttp-170) cc_final: 0.6799 (ttp80) REVERT: R 54 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7381 (ttm110) outliers start: 59 outliers final: 47 residues processed: 401 average time/residue: 0.3592 time to fit residues: 228.1199 Evaluate side-chains 397 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 282 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 637 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 325 HIS J 39 GLN M 95 GLN G 637 ASN O 100KASN N 95 GLN I 637 ASN P 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115375 restraints weight = 30244.492| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.21 r_work: 0.3202 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25392 Z= 0.149 Angle : 0.550 12.663 34572 Z= 0.277 Chirality : 0.045 0.530 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.293 53.069 4614 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 8.97 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.07 (0.16), residues: 2994 helix: 1.97 (0.26), residues: 411 sheet: 0.98 (0.17), residues: 912 loop : 0.33 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 PHE 0.010 0.001 PHE F 383 TYR 0.012 0.001 TYR D 49 ARG 0.004 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 51) link_NAG-ASN : angle 2.69332 ( 153) link_BETA1-4 : bond 0.00370 ( 12) link_BETA1-4 : angle 1.31630 ( 36) hydrogen bonds : bond 0.03692 ( 723) hydrogen bonds : angle 4.52538 ( 1872) SS BOND : bond 0.00529 ( 48) SS BOND : angle 1.04686 ( 96) covalent geometry : bond 0.00353 (25281) covalent geometry : angle 0.51761 (34287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 361 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8488 (tttm) cc_final: 0.8156 (mttm) REVERT: A 166 ARG cc_start: 0.8536 (mtp85) cc_final: 0.7743 (ttp80) REVERT: C 82 MET cc_start: 0.8861 (ptp) cc_final: 0.8630 (mtm) REVERT: C 108 LEU cc_start: 0.8321 (tp) cc_final: 0.8057 (tp) REVERT: B 616 ASN cc_start: 0.8715 (p0) cc_final: 0.8362 (p0) REVERT: H 22 CYS cc_start: 0.7796 (t) cc_final: 0.7583 (t) REVERT: H 66 ARG cc_start: 0.7049 (ttp80) cc_final: 0.6827 (ttp-170) REVERT: L 28 ASP cc_start: 0.8831 (m-30) cc_final: 0.8431 (m-30) REVERT: L 54 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7715 (ttm110) REVERT: E 51 THR cc_start: 0.8985 (m) cc_final: 0.8732 (p) REVERT: E 110 SER cc_start: 0.8622 (t) cc_final: 0.8228 (m) REVERT: E 121 LYS cc_start: 0.8543 (tttm) cc_final: 0.8202 (mttm) REVERT: E 166 ARG cc_start: 0.8605 (mtp85) cc_final: 0.7775 (ttp80) REVERT: E 358 ILE cc_start: 0.7831 (mt) cc_final: 0.7508 (mm) REVERT: M 61 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7706 (mtm110) REVERT: Q 54 ARG cc_start: 0.7957 (ttm110) cc_final: 0.7551 (ttm110) REVERT: F 110 SER cc_start: 0.8721 (t) cc_final: 0.8359 (m) REVERT: F 166 ARG cc_start: 0.8627 (mtp85) cc_final: 0.7803 (ttp80) REVERT: F 269 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7760 (pt0) REVERT: N 47 MET cc_start: 0.8678 (mmm) cc_final: 0.8441 (mmm) REVERT: N 61 ARG cc_start: 0.8049 (mtm110) cc_final: 0.7656 (mtm110) REVERT: I 544 LEU cc_start: 0.8682 (mt) cc_final: 0.8474 (mm) REVERT: I 616 ASN cc_start: 0.8827 (p0) cc_final: 0.8583 (p0) REVERT: I 624 ASP cc_start: 0.9087 (m-30) cc_final: 0.8772 (m-30) REVERT: P 22 CYS cc_start: 0.7943 (t) cc_final: 0.7661 (t) REVERT: R 54 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7412 (ttm110) outliers start: 53 outliers final: 38 residues processed: 397 average time/residue: 0.3560 time to fit residues: 223.7732 Evaluate side-chains 383 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 27 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 113 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 95 GLN B 637 ASN H 100KASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS M 95 GLN G 637 ASN O 39 GLN K 39 GLN N 95 GLN P 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115775 restraints weight = 30353.790| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.22 r_work: 0.3207 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25392 Z= 0.138 Angle : 0.546 16.719 34572 Z= 0.272 Chirality : 0.045 0.521 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.167 52.973 4614 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.93 % Allowed : 9.61 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.09 (0.16), residues: 2994 helix: 2.04 (0.26), residues: 411 sheet: 1.08 (0.17), residues: 858 loop : 0.29 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 PHE 0.010 0.001 PHE A 383 TYR 0.013 0.001 TYR D 49 ARG 0.004 0.000 ARG H 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 51) link_NAG-ASN : angle 2.89590 ( 153) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.29546 ( 36) hydrogen bonds : bond 0.03569 ( 723) hydrogen bonds : angle 4.43614 ( 1872) SS BOND : bond 0.00535 ( 48) SS BOND : angle 1.02708 ( 96) covalent geometry : bond 0.00327 (25281) covalent geometry : angle 0.50827 (34287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9016 (m) cc_final: 0.8787 (p) REVERT: A 121 LYS cc_start: 0.8563 (tttm) cc_final: 0.8168 (mttm) REVERT: A 166 ARG cc_start: 0.8535 (mtp85) cc_final: 0.7752 (ttp80) REVERT: C 18 LEU cc_start: 0.8116 (tp) cc_final: 0.7834 (tp) REVERT: C 31 SER cc_start: 0.9149 (t) cc_final: 0.8923 (t) REVERT: C 82 MET cc_start: 0.8844 (ptp) cc_final: 0.8638 (mtm) REVERT: C 108 LEU cc_start: 0.8410 (tp) cc_final: 0.8142 (tp) REVERT: B 616 ASN cc_start: 0.8727 (p0) cc_final: 0.8369 (p0) REVERT: H 22 CYS cc_start: 0.7713 (t) cc_final: 0.7495 (t) REVERT: H 66 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6909 (ttp-170) REVERT: L 31 THR cc_start: 0.8476 (m) cc_final: 0.8028 (p) REVERT: L 54 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7705 (ttm110) REVERT: E 51 THR cc_start: 0.8916 (m) cc_final: 0.8709 (p) REVERT: E 110 SER cc_start: 0.8632 (t) cc_final: 0.8200 (m) REVERT: E 121 LYS cc_start: 0.8536 (tttm) cc_final: 0.8194 (mttm) REVERT: E 166 ARG cc_start: 0.8552 (mtp85) cc_final: 0.7664 (ttp80) REVERT: E 358 ILE cc_start: 0.7876 (mt) cc_final: 0.7551 (mm) REVERT: M 61 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7765 (mtm110) REVERT: G 616 ASN cc_start: 0.8879 (p0) cc_final: 0.8441 (p0) REVERT: Q 28 ASP cc_start: 0.8661 (m-30) cc_final: 0.8441 (m-30) REVERT: Q 33 LEU cc_start: 0.8795 (tp) cc_final: 0.8500 (tp) REVERT: Q 54 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7608 (ttm110) REVERT: F 110 SER cc_start: 0.8724 (t) cc_final: 0.8370 (m) REVERT: F 166 ARG cc_start: 0.8614 (mtp85) cc_final: 0.7842 (ttp80) REVERT: N 47 MET cc_start: 0.8645 (mmm) cc_final: 0.8404 (mmm) REVERT: N 61 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7765 (mtm110) REVERT: I 544 LEU cc_start: 0.8738 (mt) cc_final: 0.8532 (mm) REVERT: I 616 ASN cc_start: 0.8829 (p0) cc_final: 0.8565 (p0) REVERT: I 624 ASP cc_start: 0.9125 (m-30) cc_final: 0.8783 (m-30) REVERT: P 22 CYS cc_start: 0.7837 (t) cc_final: 0.7519 (t) REVERT: P 39 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: R 34 GLU cc_start: 0.7833 (tt0) cc_final: 0.7463 (tt0) REVERT: R 54 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7515 (ttm110) outliers start: 51 outliers final: 40 residues processed: 389 average time/residue: 0.3679 time to fit residues: 228.9370 Evaluate side-chains 384 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 343 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 201 optimal weight: 0.0030 chunk 131 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 171 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN H 100KASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN O 39 GLN N 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119106 restraints weight = 30419.064| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.32 r_work: 0.3269 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25392 Z= 0.102 Angle : 0.519 16.428 34572 Z= 0.259 Chirality : 0.044 0.519 3963 Planarity : 0.003 0.036 4299 Dihedral : 4.996 52.791 4614 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.55 % Allowed : 9.99 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.17 (0.16), residues: 2994 helix: 2.20 (0.26), residues: 411 sheet: 1.13 (0.17), residues: 858 loop : 0.32 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.002 0.000 HIS H 35 PHE 0.010 0.001 PHE L 98 TYR 0.014 0.001 TYR D 49 ARG 0.003 0.000 ARG E 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 51) link_NAG-ASN : angle 2.76069 ( 153) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.22607 ( 36) hydrogen bonds : bond 0.03257 ( 723) hydrogen bonds : angle 4.29856 ( 1872) SS BOND : bond 0.00323 ( 48) SS BOND : angle 0.93201 ( 96) covalent geometry : bond 0.00229 (25281) covalent geometry : angle 0.48288 (34287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8995 (m) cc_final: 0.8785 (p) REVERT: A 121 LYS cc_start: 0.8547 (tttm) cc_final: 0.8133 (mttm) REVERT: A 166 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7721 (ttp80) REVERT: C 18 LEU cc_start: 0.8123 (tp) cc_final: 0.7816 (tp) REVERT: C 82 MET cc_start: 0.8843 (ptp) cc_final: 0.8593 (mtm) REVERT: C 108 LEU cc_start: 0.8448 (tp) cc_final: 0.8172 (tp) REVERT: D 61 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7963 (mtm110) REVERT: B 616 ASN cc_start: 0.8728 (p0) cc_final: 0.8371 (p0) REVERT: H 22 CYS cc_start: 0.7626 (t) cc_final: 0.7390 (t) REVERT: H 66 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6897 (ttp-170) REVERT: L 4 MET cc_start: 0.7453 (mpp) cc_final: 0.7128 (mpp) REVERT: L 31 THR cc_start: 0.8462 (m) cc_final: 0.8064 (p) REVERT: E 82 GLN cc_start: 0.7160 (tt0) cc_final: 0.6955 (tt0) REVERT: E 110 SER cc_start: 0.8574 (t) cc_final: 0.8175 (m) REVERT: E 121 LYS cc_start: 0.8511 (tttm) cc_final: 0.8165 (mttm) REVERT: E 166 ARG cc_start: 0.8505 (mtp85) cc_final: 0.7674 (ttp80) REVERT: E 358 ILE cc_start: 0.7847 (mt) cc_final: 0.7524 (mm) REVERT: M 61 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7726 (mtm110) REVERT: G 616 ASN cc_start: 0.8869 (p0) cc_final: 0.8429 (p0) REVERT: G 624 ASP cc_start: 0.8978 (m-30) cc_final: 0.8745 (m-30) REVERT: Q 28 ASP cc_start: 0.8632 (m-30) cc_final: 0.8403 (m-30) REVERT: Q 33 LEU cc_start: 0.8821 (tp) cc_final: 0.8505 (tp) REVERT: Q 54 ARG cc_start: 0.8004 (ttm110) cc_final: 0.7597 (ttm110) REVERT: F 106 GLU cc_start: 0.8125 (mp0) cc_final: 0.7838 (mp0) REVERT: F 110 SER cc_start: 0.8645 (t) cc_final: 0.8285 (m) REVERT: F 166 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7802 (ttp80) REVERT: K 27 TYR cc_start: 0.8097 (p90) cc_final: 0.7721 (p90) REVERT: N 47 MET cc_start: 0.8608 (mmm) cc_final: 0.8362 (mmm) REVERT: N 61 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7622 (mtm110) REVERT: I 616 ASN cc_start: 0.8769 (p0) cc_final: 0.8486 (p0) REVERT: I 624 ASP cc_start: 0.9107 (m-30) cc_final: 0.8777 (m-30) REVERT: P 22 CYS cc_start: 0.7672 (t) cc_final: 0.7346 (t) REVERT: R 54 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7400 (ttm110) outliers start: 41 outliers final: 34 residues processed: 390 average time/residue: 0.3533 time to fit residues: 218.3628 Evaluate side-chains 382 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 348 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 206 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 637 ASN O 39 GLN N 95 GLN P 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116001 restraints weight = 30629.961| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.32 r_work: 0.3190 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25392 Z= 0.205 Angle : 0.602 17.666 34572 Z= 0.298 Chirality : 0.047 0.504 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.240 53.418 4614 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.93 % Allowed : 9.91 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.01 (0.16), residues: 2994 helix: 1.95 (0.26), residues: 411 sheet: 0.94 (0.17), residues: 924 loop : 0.27 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 96 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.002 PHE A 383 TYR 0.012 0.002 TYR A 319 ARG 0.006 0.001 ARG R 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 51) link_NAG-ASN : angle 3.17559 ( 153) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.42273 ( 36) hydrogen bonds : bond 0.03931 ( 723) hydrogen bonds : angle 4.42730 ( 1872) SS BOND : bond 0.00507 ( 48) SS BOND : angle 1.30768 ( 96) covalent geometry : bond 0.00497 (25281) covalent geometry : angle 0.55958 (34287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 347 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8514 (tttm) cc_final: 0.8127 (mttm) REVERT: A 166 ARG cc_start: 0.8570 (mtp85) cc_final: 0.7790 (ttp80) REVERT: A 195 ASN cc_start: 0.8685 (p0) cc_final: 0.8472 (p0) REVERT: C 82 MET cc_start: 0.8844 (ptp) cc_final: 0.8642 (mtm) REVERT: B 616 ASN cc_start: 0.8831 (p0) cc_final: 0.8441 (p0) REVERT: H 22 CYS cc_start: 0.7761 (t) cc_final: 0.7544 (t) REVERT: H 66 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6690 (ttp80) REVERT: L 4 MET cc_start: 0.7447 (mpp) cc_final: 0.7169 (mpp) REVERT: L 31 THR cc_start: 0.8523 (m) cc_final: 0.8073 (p) REVERT: E 110 SER cc_start: 0.8677 (t) cc_final: 0.8228 (m) REVERT: E 121 LYS cc_start: 0.8579 (tttm) cc_final: 0.8234 (mttm) REVERT: E 166 ARG cc_start: 0.8625 (mtp85) cc_final: 0.7842 (ttp80) REVERT: J 31 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8876 (t) REVERT: M 61 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7832 (mtm110) REVERT: G 616 ASN cc_start: 0.8925 (p0) cc_final: 0.8472 (p0) REVERT: G 624 ASP cc_start: 0.8943 (m-30) cc_final: 0.8738 (m-30) REVERT: O 39 GLN cc_start: 0.7747 (tt0) cc_final: 0.7541 (tt0) REVERT: Q 31 THR cc_start: 0.8463 (m) cc_final: 0.7985 (p) REVERT: Q 33 LEU cc_start: 0.8855 (tp) cc_final: 0.8565 (tp) REVERT: Q 54 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7706 (ttm110) REVERT: F 106 GLU cc_start: 0.8136 (mp0) cc_final: 0.7817 (mp0) REVERT: F 110 SER cc_start: 0.8743 (t) cc_final: 0.8376 (m) REVERT: F 166 ARG cc_start: 0.8572 (mtp85) cc_final: 0.7833 (ttp80) REVERT: K 27 TYR cc_start: 0.8127 (p90) cc_final: 0.7741 (p90) REVERT: N 47 MET cc_start: 0.8655 (mmm) cc_final: 0.8420 (mmm) REVERT: N 61 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7720 (mtm110) REVERT: I 544 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8210 (mm) REVERT: I 616 ASN cc_start: 0.8803 (p0) cc_final: 0.8488 (p0) REVERT: I 624 ASP cc_start: 0.9103 (m-30) cc_final: 0.8759 (m-30) REVERT: P 22 CYS cc_start: 0.7800 (t) cc_final: 0.7511 (t) REVERT: R 34 GLU cc_start: 0.7935 (tt0) cc_final: 0.7629 (tt0) REVERT: R 54 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7436 (ttm110) outliers start: 51 outliers final: 45 residues processed: 384 average time/residue: 0.3569 time to fit residues: 215.9725 Evaluate side-chains 384 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 188 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN Q 90 GLN N 95 GLN P 39 GLN P 100KASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117048 restraints weight = 30525.015| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.31 r_work: 0.3204 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25392 Z= 0.168 Angle : 0.578 16.776 34572 Z= 0.288 Chirality : 0.046 0.581 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.265 53.319 4614 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.85 % Allowed : 10.52 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.95 (0.16), residues: 2994 helix: 1.97 (0.26), residues: 411 sheet: 0.89 (0.17), residues: 924 loop : 0.23 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 96 HIS 0.003 0.001 HIS E 105 PHE 0.013 0.001 PHE J 67 TYR 0.013 0.001 TYR H 79 ARG 0.004 0.000 ARG F 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00636 ( 51) link_NAG-ASN : angle 3.03628 ( 153) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.35080 ( 36) hydrogen bonds : bond 0.03713 ( 723) hydrogen bonds : angle 4.39008 ( 1872) SS BOND : bond 0.00493 ( 48) SS BOND : angle 1.23820 ( 96) covalent geometry : bond 0.00407 (25281) covalent geometry : angle 0.53819 (34287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5988 Ramachandran restraints generated. 2994 Oldfield, 0 Emsley, 2994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8530 (tttm) cc_final: 0.8114 (mttm) REVERT: A 166 ARG cc_start: 0.8596 (mtp85) cc_final: 0.7811 (ttp80) REVERT: C 82 MET cc_start: 0.8839 (ptp) cc_final: 0.8614 (mtm) REVERT: B 616 ASN cc_start: 0.8801 (p0) cc_final: 0.8447 (p0) REVERT: H 66 ARG cc_start: 0.7133 (ttp80) cc_final: 0.6853 (ttp-170) REVERT: L 4 MET cc_start: 0.7475 (mpp) cc_final: 0.7194 (mpp) REVERT: L 31 THR cc_start: 0.8510 (m) cc_final: 0.8069 (p) REVERT: E 110 SER cc_start: 0.8667 (t) cc_final: 0.8217 (m) REVERT: E 121 LYS cc_start: 0.8562 (tttm) cc_final: 0.8240 (mttm) REVERT: E 150 MET cc_start: 0.8958 (mtm) cc_final: 0.8575 (mtp) REVERT: E 166 ARG cc_start: 0.8549 (mtp85) cc_final: 0.7747 (ttp80) REVERT: J 31 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8886 (t) REVERT: M 61 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7884 (mtm110) REVERT: G 616 ASN cc_start: 0.8898 (p0) cc_final: 0.8455 (p0) REVERT: O 39 GLN cc_start: 0.7642 (tt0) cc_final: 0.7355 (tt0) REVERT: Q 33 LEU cc_start: 0.8847 (tp) cc_final: 0.8531 (tp) REVERT: F 106 GLU cc_start: 0.8172 (mp0) cc_final: 0.7873 (mp0) REVERT: F 110 SER cc_start: 0.8732 (t) cc_final: 0.8379 (m) REVERT: F 166 ARG cc_start: 0.8628 (mtp85) cc_final: 0.7909 (ttp80) REVERT: K 27 TYR cc_start: 0.8164 (p90) cc_final: 0.7779 (p90) REVERT: N 47 MET cc_start: 0.8624 (mmm) cc_final: 0.8386 (mmm) REVERT: N 61 ARG cc_start: 0.8177 (mtm110) cc_final: 0.7729 (mtm110) REVERT: I 544 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8179 (mm) REVERT: I 616 ASN cc_start: 0.8808 (p0) cc_final: 0.8519 (p0) REVERT: I 624 ASP cc_start: 0.9097 (m-30) cc_final: 0.8724 (m-30) REVERT: P 22 CYS cc_start: 0.7718 (t) cc_final: 0.7422 (t) REVERT: R 34 GLU cc_start: 0.7951 (tt0) cc_final: 0.7647 (tt0) REVERT: R 54 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7489 (ttm110) outliers start: 49 outliers final: 43 residues processed: 371 average time/residue: 0.3591 time to fit residues: 213.7143 Evaluate side-chains 375 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN Q 90 GLN N 95 GLN P 100KASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114987 restraints weight = 30587.642| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.42 r_work: 0.3182 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25392 Z= 0.201 Angle : 0.605 17.080 34572 Z= 0.300 Chirality : 0.047 0.552 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.386 53.579 4614 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.89 % Allowed : 10.48 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.16), residues: 2994 helix: 1.87 (0.26), residues: 411 sheet: 0.80 (0.17), residues: 924 loop : 0.15 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE J 67 TYR 0.014 0.002 TYR H 79 ARG 0.008 0.000 ARG D 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 51) link_NAG-ASN : angle 3.11220 ( 153) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 1.41250 ( 36) hydrogen bonds : bond 0.03932 ( 723) hydrogen bonds : angle 4.46738 ( 1872) SS BOND : bond 0.00510 ( 48) SS BOND : angle 1.41189 ( 96) covalent geometry : bond 0.00488 (25281) covalent geometry : angle 0.56403 (34287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15028.21 seconds wall clock time: 260 minutes 15.68 seconds (15615.68 seconds total)