Starting phenix.real_space_refine on Sat Jun 21 05:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4d_41027/06_2025/8t4d_41027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4d_41027/06_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_41027/06_2025/8t4d_41027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4d_41027/06_2025/8t4d_41027.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4d_41027/06_2025/8t4d_41027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4d_41027/06_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-5710/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: 15.90, per 1000 atoms: 0.64 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: 6.01 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: 3.29 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: 8.29 Time building geometry restraints manager: 7.12 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain '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: 5.420 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: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 56.420 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.700 ------------------------------------------------------------------------------- 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 : 3.011 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: 0.4615 time to fit residues: 434.2834 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 : 2.635 ------------------------------------------------------------------------------- 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 = 0.124186 restraints weight = 30308.054| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.46 r_work: 0.3292 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.37 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 12.591 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 2.86795 ( 153) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 1.68545 ( 36) hydrogen bonds : bond 0.04429 ( 723) hydrogen bonds : angle 5.08548 ( 1872) SS BOND : bond 0.00563 ( 48) SS BOND : angle 1.21742 ( 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 : 2.604 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: 0.8490 (mtp85) cc_final: 0.7813 (mtm110) REVERT: C 18 LEU cc_start: 0.8333 (tp) cc_final: 0.8046 (tp) REVERT: H 39 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: L 54 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7609 (ttm110) REVERT: E 110 SER cc_start: 0.8602 (t) cc_final: 0.8269 (m) REVERT: E 123 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8944 (p) REVERT: E 166 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7637 (ttp80) REVERT: J 66 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7752 (mtm110) REVERT: M 47 MET cc_start: 0.8774 (mmm) cc_final: 0.8529 (mmt) REVERT: M 52 THR cc_start: 0.8488 (p) cc_final: 0.8233 (m) REVERT: O 39 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: O 77 THR cc_start: 0.8656 (m) cc_final: 0.8307 (p) REVERT: O 105 ARG cc_start: 0.7876 (ptp90) cc_final: 0.7655 (ptp90) REVERT: Q 28 ASP cc_start: 0.8623 (m-30) cc_final: 0.8401 (m-30) REVERT: Q 33 LEU cc_start: 0.8717 (tp) cc_final: 0.8481 (tp) REVERT: Q 54 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7362 (ttm110) REVERT: F 110 SER cc_start: 0.8629 (t) cc_final: 0.8257 (m) REVERT: F 166 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7727 (mtm110) REVERT: F 199 SER cc_start: 0.8967 (p) cc_final: 0.8572 (p) REVERT: F 269 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7752 (pt0) REVERT: N 47 MET cc_start: 0.8719 (mmm) cc_final: 0.8301 (mmt) REVERT: I 624 ASP cc_start: 0.9002 (m-30) cc_final: 0.8748 (m-30) outliers start: 58 outliers final: 38 residues processed: 455 average time/residue: 0.3941 time to fit residues: 278.0344 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 : 2.866 ------------------------------------------------------------------------------- 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: 4.9990 chunk 204 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 H 39 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.159846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123973 restraints weight = 30351.511| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.38 r_work: 0.3298 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25392 Z= 0.140 Angle : 0.574 14.230 34572 Z= 0.291 Chirality : 0.046 0.480 3963 Planarity : 0.004 0.049 4299 Dihedral : 6.031 52.697 4614 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.78 % Allowed : 7.45 % Favored : 90.77 % 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 (0.15), residues: 2994 helix: 2.09 (0.27), residues: 411 sheet: 1.39 (0.16), residues: 897 loop : 0.50 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 50 HIS 0.003 0.001 HIS E 105 PHE 0.015 0.001 PHE H 100B TYR 0.014 0.001 TYR J 27 ARG 0.004 0.000 ARG E 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 51) link_NAG-ASN : angle 2.66764 ( 153) link_BETA1-4 : bond 0.00424 ( 12) link_BETA1-4 : angle 1.46839 ( 36) hydrogen bonds : bond 0.03850 ( 723) hydrogen bonds : angle 4.75546 ( 1872) SS BOND : bond 0.00453 ( 48) SS BOND : angle 1.05475 ( 96) covalent geometry : bond 0.00325 (25281) covalent geometry : angle 0.54301 (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 440 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 393 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8589 (tttm) cc_final: 0.8228 (mttm) REVERT: A 123 THR cc_start: 0.9134 (m) cc_final: 0.8896 (p) REVERT: A 166 ARG cc_start: 0.8514 (mtp85) cc_final: 0.7652 (ttp80) REVERT: C 82 MET cc_start: 0.8765 (ptp) cc_final: 0.8514 (mtm) REVERT: H 39 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: H 66 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6918 (ttp-170) REVERT: H 77 THR cc_start: 0.8618 (m) cc_final: 0.8324 (p) REVERT: H 105 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7674 (ptp90) REVERT: L 28 ASP cc_start: 0.8711 (m-30) cc_final: 0.8296 (m-30) REVERT: L 54 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7672 (ttm110) REVERT: E 110 SER cc_start: 0.8594 (t) cc_final: 0.8241 (m) REVERT: E 166 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7674 (ttp80) REVERT: E 269 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7769 (pt0) REVERT: M 52 THR cc_start: 0.8550 (p) cc_final: 0.8291 (m) REVERT: O 77 THR cc_start: 0.8605 (m) cc_final: 0.8394 (p) REVERT: Q 28 ASP cc_start: 0.8606 (m-30) cc_final: 0.8015 (m-30) REVERT: Q 31 THR cc_start: 0.8368 (m) cc_final: 0.7801 (p) REVERT: Q 33 LEU cc_start: 0.8807 (tp) cc_final: 0.8542 (tp) REVERT: Q 54 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7521 (ttm110) REVERT: F 110 SER cc_start: 0.8602 (t) cc_final: 0.8249 (m) REVERT: F 166 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7597 (ttp80) REVERT: F 199 SER cc_start: 0.9072 (p) cc_final: 0.8685 (p) REVERT: F 269 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7687 (pt0) REVERT: F 432 GLN cc_start: 0.8410 (mt0) cc_final: 0.8164 (mt0) REVERT: N 47 MET cc_start: 0.8665 (mmm) cc_final: 0.8338 (mmm) REVERT: I 624 ASP cc_start: 0.9057 (m-30) cc_final: 0.8731 (m-30) REVERT: R 28 ASP cc_start: 0.8625 (m-30) cc_final: 0.8424 (m-30) REVERT: R 54 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7361 (ttm110) outliers start: 47 outliers final: 34 residues processed: 422 average time/residue: 0.5212 time to fit residues: 346.5720 Evaluate side-chains 401 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN 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 D residue 27 ASP Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 39 GLN 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: 0.7980 chunk 228 optimal weight: 0.3980 chunk 278 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 39 HIS 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 P 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120225 restraints weight = 30660.571| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.38 r_work: 0.3279 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 25392 Z= 0.148 Angle : 0.553 10.529 34572 Z= 0.281 Chirality : 0.045 0.434 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.458 52.736 4614 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.82 % Allowed : 8.63 % Favored : 89.56 % 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: 1.34 (0.16), residues: 2994 helix: 2.04 (0.26), residues: 411 sheet: 1.20 (0.16), residues: 933 loop : 0.51 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 50 HIS 0.003 0.001 HIS F 105 PHE 0.011 0.001 PHE Q 36 TYR 0.010 0.001 TYR D 96 ARG 0.003 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 51) link_NAG-ASN : angle 2.49807 ( 153) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.38873 ( 36) hydrogen bonds : bond 0.03709 ( 723) hydrogen bonds : angle 4.61800 ( 1872) SS BOND : bond 0.00528 ( 48) SS BOND : angle 1.05221 ( 96) covalent geometry : bond 0.00350 (25281) covalent geometry : angle 0.52467 (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 425 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8554 (tttm) cc_final: 0.8204 (mttm) REVERT: A 166 ARG cc_start: 0.8499 (mtp85) cc_final: 0.7827 (mtm110) REVERT: C 82 MET cc_start: 0.8863 (ptp) cc_final: 0.8631 (mtm) REVERT: B 616 ASN cc_start: 0.8752 (p0) cc_final: 0.8490 (p0) REVERT: H 77 THR cc_start: 0.8639 (m) cc_final: 0.8366 (p) REVERT: L 28 ASP cc_start: 0.8762 (m-30) cc_final: 0.8371 (m-30) REVERT: L 54 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7689 (ttm110) REVERT: E 110 SER cc_start: 0.8623 (t) cc_final: 0.8238 (m) REVERT: E 166 ARG cc_start: 0.8531 (mtp85) cc_final: 0.7660 (ttp80) REVERT: E 269 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7812 (pt0) REVERT: Q 31 THR cc_start: 0.8420 (m) cc_final: 0.7829 (p) REVERT: Q 54 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7538 (ttm110) REVERT: F 110 SER cc_start: 0.8671 (t) cc_final: 0.8316 (m) REVERT: F 166 ARG cc_start: 0.8536 (mtp85) cc_final: 0.7713 (ttp80) REVERT: F 269 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7727 (pt0) REVERT: N 47 MET cc_start: 0.8658 (mmm) cc_final: 0.8422 (mmt) REVERT: I 624 ASP cc_start: 0.9071 (m-30) cc_final: 0.8784 (m-30) REVERT: R 54 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7314 (ttm110) outliers start: 48 outliers final: 39 residues processed: 413 average time/residue: 0.4048 time to fit residues: 264.2505 Evaluate side-chains 397 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 2.947 ------------------------------------------------------------------------------- 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 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 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 45 LEU 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 F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 158 SER 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 48 VAL Chi-restraints excluded: chain K residue 76 ASN 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=3.50 ------------------------------------------------------------------------------- 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: 0.8980 chunk 108 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 238 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 H 39 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119315 restraints weight = 30641.530| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.37 r_work: 0.3263 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2744 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 : 0.552 14.279 34572 Z= 0.278 Chirality : 0.045 0.528 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.304 52.912 4614 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.08 % Allowed : 8.63 % Favored : 89.29 % 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: 1.22 (0.16), residues: 2994 helix: 2.04 (0.26), residues: 411 sheet: 1.02 (0.16), residues: 951 loop : 0.46 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE J 67 TYR 0.011 0.001 TYR M 49 ARG 0.004 0.000 ARG O 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 51) link_NAG-ASN : angle 2.74386 ( 153) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.33026 ( 36) hydrogen bonds : bond 0.03683 ( 723) hydrogen bonds : angle 4.53026 ( 1872) SS BOND : bond 0.00422 ( 48) SS BOND : angle 1.00437 ( 96) covalent geometry : bond 0.00355 (25281) covalent geometry : angle 0.51838 (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 412 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8501 (tttm) cc_final: 0.8176 (mttm) REVERT: A 166 ARG cc_start: 0.8564 (mtp85) cc_final: 0.7679 (ttp80) REVERT: C 82 MET cc_start: 0.8894 (ptp) cc_final: 0.8657 (mtm) REVERT: B 616 ASN cc_start: 0.8745 (p0) cc_final: 0.8485 (p0) REVERT: H 22 CYS cc_start: 0.7785 (t) cc_final: 0.7569 (t) REVERT: H 77 THR cc_start: 0.8646 (m) cc_final: 0.8368 (p) REVERT: L 28 ASP cc_start: 0.8771 (m-30) cc_final: 0.8394 (m-30) REVERT: L 54 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7724 (ttm110) REVERT: E 110 SER cc_start: 0.8622 (t) cc_final: 0.8244 (m) REVERT: E 166 ARG cc_start: 0.8555 (mtp85) cc_final: 0.7706 (ttp80) REVERT: Q 31 THR cc_start: 0.8405 (m) cc_final: 0.7847 (p) REVERT: Q 33 LEU cc_start: 0.8873 (tp) cc_final: 0.8620 (tp) REVERT: Q 54 ARG cc_start: 0.7949 (ttm110) cc_final: 0.7548 (ttm110) REVERT: F 110 SER cc_start: 0.8738 (t) cc_final: 0.8384 (m) REVERT: F 166 ARG cc_start: 0.8546 (mtp85) cc_final: 0.7862 (mtm110) REVERT: F 269 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7754 (pt0) REVERT: N 47 MET cc_start: 0.8652 (mmm) cc_final: 0.8436 (mmt) REVERT: N 61 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7688 (mtm110) REVERT: I 616 ASN cc_start: 0.8826 (p0) cc_final: 0.8591 (p0) REVERT: I 624 ASP cc_start: 0.9067 (m-30) cc_final: 0.8785 (m-30) REVERT: P 22 CYS cc_start: 0.7851 (t) cc_final: 0.7575 (t) REVERT: R 54 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7364 (ttm110) outliers start: 55 outliers final: 41 residues processed: 396 average time/residue: 0.4229 time to fit residues: 268.4510 Evaluate side-chains 388 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 ASN 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 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 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 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 45 LEU 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 121 LYS Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL 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 31 SER Chi-restraints excluded: chain K residue 48 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 75 THR 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: 2.9990 chunk 266 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** E 325 HIS E 374 HIS J 39 GLN M 39 HIS M 95 GLN O 39 GLN O 100KASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS K 39 GLN N 95 GLN P 39 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113298 restraints weight = 30653.126| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.43 r_work: 0.3128 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 25392 Z= 0.296 Angle : 0.681 15.009 34572 Z= 0.341 Chirality : 0.050 0.493 3963 Planarity : 0.005 0.043 4299 Dihedral : 5.761 53.936 4614 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.35 % Allowed : 8.89 % Favored : 88.76 % 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: 0.73 (0.15), residues: 2994 helix: 1.54 (0.26), residues: 411 sheet: 0.77 (0.17), residues: 936 loop : 0.13 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 47 HIS 0.005 0.002 HIS E 374 PHE 0.022 0.002 PHE A 383 TYR 0.016 0.002 TYR F 319 ARG 0.005 0.001 ARG F 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 51) link_NAG-ASN : angle 3.14152 ( 153) link_BETA1-4 : bond 0.00323 ( 12) link_BETA1-4 : angle 1.54862 ( 36) hydrogen bonds : bond 0.04623 ( 723) hydrogen bonds : angle 4.82545 ( 1872) SS BOND : bond 0.00513 ( 48) SS BOND : angle 1.38020 ( 96) covalent geometry : bond 0.00720 (25281) covalent geometry : angle 0.64523 (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 426 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8559 (tttm) cc_final: 0.8190 (mttm) REVERT: A 166 ARG cc_start: 0.8562 (mtp85) cc_final: 0.7780 (ttp80) REVERT: C 31 SER cc_start: 0.9216 (t) cc_final: 0.8954 (t) REVERT: B 616 ASN cc_start: 0.8799 (p0) cc_final: 0.8423 (p0) REVERT: H 80 MET cc_start: 0.7854 (ttp) cc_final: 0.7516 (ttp) REVERT: H 105 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7746 (ptp90) REVERT: L 4 MET cc_start: 0.7481 (mpp) cc_final: 0.7177 (mpp) REVERT: L 28 ASP cc_start: 0.8886 (m-30) cc_final: 0.8462 (m-30) REVERT: L 54 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7714 (ttm110) REVERT: E 110 SER cc_start: 0.8769 (t) cc_final: 0.8325 (m) REVERT: E 166 ARG cc_start: 0.8638 (mtp85) cc_final: 0.7816 (ttp80) REVERT: E 432 GLN cc_start: 0.8670 (mt0) cc_final: 0.8347 (mt0) REVERT: J 31 SER cc_start: 0.9133 (t) cc_final: 0.8873 (t) REVERT: G 616 ASN cc_start: 0.8911 (p0) cc_final: 0.8443 (p0) REVERT: Q 28 ASP cc_start: 0.8802 (m-30) cc_final: 0.8545 (m-30) REVERT: Q 54 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7719 (ttm110) REVERT: F 110 SER cc_start: 0.8734 (t) cc_final: 0.8332 (m) REVERT: F 166 ARG cc_start: 0.8610 (mtp85) cc_final: 0.7824 (ttp80) REVERT: F 269 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7794 (pt0) REVERT: N 47 MET cc_start: 0.8724 (mmm) cc_final: 0.8454 (mmm) REVERT: N 61 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7622 (mtm110) REVERT: I 616 ASN cc_start: 0.8905 (p0) cc_final: 0.8617 (p0) REVERT: I 624 ASP cc_start: 0.9026 (m-30) cc_final: 0.8685 (m-30) REVERT: P 66 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6767 (ttp80) REVERT: R 54 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7472 (ttm110) outliers start: 62 outliers final: 47 residues processed: 406 average time/residue: 0.3598 time to fit residues: 230.2668 Evaluate side-chains 394 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 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 375 SER Chi-restraints excluded: chain E residue 426 MET 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 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 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 442 VAL Chi-restraints excluded: chain K residue 48 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 27 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 637 ASN H 100KASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN M 95 GLN G 637 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 575 GLN I 652 GLN P 100KASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114187 restraints weight = 30447.587| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.21 r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3237 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= 0.153 Angle : 0.567 15.985 34572 Z= 0.285 Chirality : 0.045 0.514 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.490 53.262 4614 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.16 % Allowed : 9.61 % Favored : 88.23 % 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: 0.81 (0.15), residues: 2994 helix: 1.79 (0.26), residues: 411 sheet: 0.72 (0.17), residues: 933 loop : 0.20 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS A 72 PHE 0.011 0.001 PHE C 67 TYR 0.014 0.001 TYR M 96 ARG 0.004 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 51) link_NAG-ASN : angle 2.87747 ( 153) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.29329 ( 36) hydrogen bonds : bond 0.03770 ( 723) hydrogen bonds : angle 4.61327 ( 1872) SS BOND : bond 0.00537 ( 48) SS BOND : angle 1.17655 ( 96) covalent geometry : bond 0.00364 (25281) covalent geometry : angle 0.53076 (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 418 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 361 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9041 (m) cc_final: 0.8837 (p) REVERT: A 74 CYS cc_start: 0.7368 (m) cc_final: 0.7096 (m) REVERT: A 121 LYS cc_start: 0.8508 (tttm) cc_final: 0.8136 (mttm) REVERT: A 166 ARG cc_start: 0.8563 (mtp85) cc_final: 0.7804 (ttp80) REVERT: C 31 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8938 (t) REVERT: D 39 HIS cc_start: 0.8402 (m-70) cc_final: 0.8166 (m90) REVERT: D 61 ARG cc_start: 0.8247 (mtm110) cc_final: 0.7974 (mtm110) REVERT: B 616 ASN cc_start: 0.8782 (p0) cc_final: 0.8441 (p0) REVERT: H 105 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7672 (ptp90) REVERT: L 54 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7724 (ttm110) REVERT: E 110 SER cc_start: 0.8660 (t) cc_final: 0.8213 (m) REVERT: E 121 LYS cc_start: 0.8553 (tttm) cc_final: 0.8217 (mttm) REVERT: E 166 ARG cc_start: 0.8594 (mtp85) cc_final: 0.7822 (ttp80) REVERT: E 358 ILE cc_start: 0.7955 (mt) cc_final: 0.7635 (mm) REVERT: E 432 GLN cc_start: 0.8623 (mt0) cc_final: 0.8317 (mt0) REVERT: J 31 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8871 (t) REVERT: M 61 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7593 (mtm110) REVERT: G 616 ASN cc_start: 0.8867 (p0) cc_final: 0.8440 (p0) REVERT: Q 28 ASP cc_start: 0.8722 (m-30) cc_final: 0.8510 (m-30) REVERT: Q 54 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7756 (ttm110) REVERT: F 110 SER cc_start: 0.8681 (t) cc_final: 0.8303 (m) REVERT: F 166 ARG cc_start: 0.8591 (mtp85) cc_final: 0.7912 (ttp-110) REVERT: F 269 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7764 (pt0) REVERT: N 47 MET cc_start: 0.8685 (mmm) cc_final: 0.8448 (mmm) REVERT: N 61 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7707 (mtm110) REVERT: I 616 ASN cc_start: 0.8879 (p0) cc_final: 0.8605 (p0) REVERT: I 624 ASP cc_start: 0.9094 (m-30) cc_final: 0.8750 (m-30) REVERT: P 22 CYS cc_start: 0.7938 (t) cc_final: 0.7630 (t) REVERT: P 66 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6873 (ttp80) REVERT: R 54 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7470 (ttm110) outliers start: 57 outliers final: 44 residues processed: 399 average time/residue: 0.3561 time to fit residues: 225.4861 Evaluate side-chains 387 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 103 GLN 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 31 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 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 241 ASN Chi-restraints excluded: chain E residue 325 HIS 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 M residue 27 ASP Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain O residue 48 MET 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 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 442 VAL Chi-restraints excluded: chain K residue 48 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 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 33 LEU Chi-restraints excluded: chain R residue 58 VAL 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: 0.8980 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 106 optimal weight: 0.0570 chunk 171 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.4708 ------------------------------------------------------------------------------- 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** D 53 GLN B 637 ASN H 39 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN O 39 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 637 ASN P 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117530 restraints weight = 30456.950| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.32 r_work: 0.3252 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25392 Z= 0.112 Angle : 0.533 15.284 34572 Z= 0.266 Chirality : 0.044 0.423 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.173 52.912 4614 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.01 % Allowed : 10.22 % Favored : 87.78 % 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: 0.98 (0.16), residues: 2994 helix: 2.06 (0.26), residues: 411 sheet: 0.88 (0.17), residues: 879 loop : 0.26 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 36 HIS 0.002 0.001 HIS A 105 PHE 0.014 0.001 PHE C 67 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG F 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 51) link_NAG-ASN : angle 2.69488 ( 153) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.26189 ( 36) hydrogen bonds : bond 0.03369 ( 723) hydrogen bonds : angle 4.39288 ( 1872) SS BOND : bond 0.00508 ( 48) SS BOND : angle 1.20678 ( 96) covalent geometry : bond 0.00260 (25281) covalent geometry : angle 0.49800 (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 401 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7165 (m) cc_final: 0.6794 (m) REVERT: A 121 LYS cc_start: 0.8464 (tttm) cc_final: 0.8108 (mttm) REVERT: A 166 ARG cc_start: 0.8536 (mtp85) cc_final: 0.7750 (ttp80) REVERT: A 434 MET cc_start: 0.9348 (ttp) cc_final: 0.9002 (ttp) REVERT: C 31 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8920 (t) REVERT: D 39 HIS cc_start: 0.8411 (m-70) cc_final: 0.8196 (m90) REVERT: B 616 ASN cc_start: 0.8780 (p0) cc_final: 0.8445 (p0) REVERT: L 4 MET cc_start: 0.7389 (mpp) cc_final: 0.7083 (mpp) REVERT: L 31 THR cc_start: 0.8481 (m) cc_final: 0.8081 (p) REVERT: L 54 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7439 (ttm110) REVERT: E 110 SER cc_start: 0.8614 (t) cc_final: 0.8201 (m) REVERT: E 166 ARG cc_start: 0.8533 (mtp85) cc_final: 0.7711 (ttp80) REVERT: E 358 ILE cc_start: 0.7924 (mt) cc_final: 0.7606 (mm) REVERT: E 432 GLN cc_start: 0.8583 (mt0) cc_final: 0.8267 (mt0) REVERT: J 31 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8868 (t) REVERT: M 61 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7432 (mtm110) REVERT: G 616 ASN cc_start: 0.8855 (p0) cc_final: 0.8429 (p0) REVERT: Q 54 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7678 (ttm110) REVERT: F 106 GLU cc_start: 0.8153 (mp0) cc_final: 0.7865 (mp0) REVERT: F 110 SER cc_start: 0.8713 (t) cc_final: 0.8343 (m) REVERT: F 166 ARG cc_start: 0.8558 (mtp85) cc_final: 0.7840 (ttp80) REVERT: N 47 MET cc_start: 0.8624 (mmm) cc_final: 0.8387 (mmm) REVERT: N 61 ARG cc_start: 0.8169 (mtm110) cc_final: 0.7684 (mtm110) REVERT: I 616 ASN cc_start: 0.8841 (p0) cc_final: 0.8557 (p0) REVERT: I 624 ASP cc_start: 0.9117 (m-30) cc_final: 0.8780 (m-30) REVERT: P 22 CYS cc_start: 0.7676 (t) cc_final: 0.7349 (t) REVERT: P 66 ARG cc_start: 0.7129 (ttp-170) cc_final: 0.6917 (ttp80) REVERT: P 77 THR cc_start: 0.8626 (m) cc_final: 0.8293 (p) REVERT: R 54 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7483 (ttm110) outliers start: 53 outliers final: 39 residues processed: 383 average time/residue: 0.3638 time to fit residues: 221.1255 Evaluate side-chains 379 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 103 GLN 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 31 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 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 241 ASN Chi-restraints excluded: chain E residue 325 HIS 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 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 48 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 33 LEU 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: 1.9990 chunk 65 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 257 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** D 95 GLN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 637 ASN O 39 GLN O 100KASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116496 restraints weight = 30658.077| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.34 r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25392 Z= 0.169 Angle : 0.578 17.127 34572 Z= 0.286 Chirality : 0.046 0.528 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.230 53.263 4614 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.12 % Allowed : 10.25 % Favored : 87.63 % 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: 0.93 (0.16), residues: 2994 helix: 1.98 (0.26), residues: 411 sheet: 0.90 (0.17), residues: 888 loop : 0.19 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 96 HIS 0.003 0.001 HIS E 105 PHE 0.017 0.001 PHE C 67 TYR 0.014 0.001 TYR D 49 ARG 0.006 0.000 ARG R 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 51) link_NAG-ASN : angle 3.09058 ( 153) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 1.37401 ( 36) hydrogen bonds : bond 0.03729 ( 723) hydrogen bonds : angle 4.42783 ( 1872) SS BOND : bond 0.00518 ( 48) SS BOND : angle 1.37123 ( 96) covalent geometry : bond 0.00407 (25281) covalent geometry : angle 0.53584 (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 402 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 346 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7205 (m) cc_final: 0.6900 (m) REVERT: A 121 LYS cc_start: 0.8515 (tttm) cc_final: 0.8177 (mttm) REVERT: A 166 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7806 (ttp80) REVERT: A 432 GLN cc_start: 0.8509 (mt0) cc_final: 0.8178 (mt0) REVERT: C 31 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8903 (t) REVERT: D 39 HIS cc_start: 0.8424 (m-70) cc_final: 0.8185 (m90) REVERT: D 61 ARG cc_start: 0.8245 (mtm110) cc_final: 0.8014 (mtm110) REVERT: B 616 ASN cc_start: 0.8809 (p0) cc_final: 0.8467 (p0) REVERT: L 4 MET cc_start: 0.7421 (mpp) cc_final: 0.7128 (mpp) REVERT: L 31 THR cc_start: 0.8476 (m) cc_final: 0.8070 (p) REVERT: E 110 SER cc_start: 0.8686 (t) cc_final: 0.8237 (m) REVERT: E 121 LYS cc_start: 0.8579 (tttm) cc_final: 0.8235 (mttm) REVERT: E 150 MET cc_start: 0.9056 (mtp) cc_final: 0.8856 (mtm) REVERT: E 166 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7666 (ttp80) REVERT: E 432 GLN cc_start: 0.8604 (mt0) cc_final: 0.8293 (mt0) REVERT: J 31 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8888 (t) REVERT: M 61 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7817 (mtm110) REVERT: G 616 ASN cc_start: 0.8868 (p0) cc_final: 0.8434 (p0) REVERT: Q 54 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7737 (ttm110) REVERT: F 106 GLU cc_start: 0.8178 (mp0) cc_final: 0.7876 (mp0) REVERT: F 110 SER cc_start: 0.8772 (t) cc_final: 0.8404 (m) REVERT: F 166 ARG cc_start: 0.8624 (mtp85) cc_final: 0.7922 (ttp80) REVERT: N 47 MET cc_start: 0.8634 (mmm) cc_final: 0.8386 (mmm) REVERT: N 61 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7712 (mtm110) REVERT: I 616 ASN cc_start: 0.8839 (p0) cc_final: 0.8539 (p0) REVERT: I 624 ASP cc_start: 0.9103 (m-30) cc_final: 0.8736 (m-30) REVERT: P 22 CYS cc_start: 0.7750 (t) cc_final: 0.7451 (t) REVERT: P 39 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: P 66 ARG cc_start: 0.7146 (ttp-170) cc_final: 0.6925 (ttp80) REVERT: R 54 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7513 (ttm110) outliers start: 56 outliers final: 44 residues processed: 385 average time/residue: 0.3476 time to fit residues: 213.0261 Evaluate side-chains 389 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 342 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 103 GLN 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 375 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 31 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 H residue 11 VAL Chi-restraints excluded: chain H residue 92 CYS 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 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 76 ASN Chi-restraints excluded: chain M residue 27 ASP 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 442 VAL Chi-restraints excluded: chain K residue 48 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 39 GLN 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: 0.2980 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** L 38 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116111 restraints weight = 30569.482| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.30 r_work: 0.3228 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25392 Z= 0.141 Angle : 0.555 15.821 34572 Z= 0.276 Chirality : 0.045 0.512 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.174 53.257 4614 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.93 % Allowed : 10.59 % Favored : 87.48 % 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: 0.94 (0.16), residues: 2994 helix: 2.04 (0.26), residues: 411 sheet: 0.96 (0.17), residues: 858 loop : 0.18 (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 0.015 0.001 PHE C 67 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG F 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 51) link_NAG-ASN : angle 2.92546 ( 153) link_BETA1-4 : bond 0.00360 ( 12) link_BETA1-4 : angle 1.31468 ( 36) hydrogen bonds : bond 0.03534 ( 723) hydrogen bonds : angle 4.38100 ( 1872) SS BOND : bond 0.00475 ( 48) SS BOND : angle 1.36874 ( 96) covalent geometry : bond 0.00336 (25281) covalent geometry : angle 0.51543 (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 394 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 343 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6868 (m) cc_final: 0.6565 (m) REVERT: A 121 LYS cc_start: 0.8486 (tttm) cc_final: 0.8119 (mttm) REVERT: A 166 ARG cc_start: 0.8539 (mtp85) cc_final: 0.7755 (ttp-110) REVERT: A 432 GLN cc_start: 0.8500 (mt0) cc_final: 0.8157 (mt0) REVERT: C 31 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8890 (t) REVERT: D 39 HIS cc_start: 0.8416 (m-70) cc_final: 0.8177 (m90) REVERT: D 61 ARG cc_start: 0.8251 (mtm110) cc_final: 0.8037 (mtm110) REVERT: B 616 ASN cc_start: 0.8804 (p0) cc_final: 0.8459 (p0) REVERT: L 4 MET cc_start: 0.7449 (mpp) cc_final: 0.7173 (mpp) REVERT: L 31 THR cc_start: 0.8488 (m) cc_final: 0.8105 (p) REVERT: E 110 SER cc_start: 0.8650 (t) cc_final: 0.8188 (m) REVERT: E 121 LYS cc_start: 0.8559 (tttm) cc_final: 0.8203 (mttm) REVERT: E 150 MET cc_start: 0.8990 (mtp) cc_final: 0.8772 (mtm) REVERT: E 166 ARG cc_start: 0.8551 (mtp85) cc_final: 0.7667 (ttp80) REVERT: E 432 GLN cc_start: 0.8578 (mt0) cc_final: 0.8240 (mt0) REVERT: J 31 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8873 (t) REVERT: M 61 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7462 (mtm110) REVERT: G 616 ASN cc_start: 0.8877 (p0) cc_final: 0.8439 (p0) REVERT: Q 54 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7645 (ttm110) REVERT: F 106 GLU cc_start: 0.8107 (mp0) cc_final: 0.7807 (mp0) REVERT: F 110 SER cc_start: 0.8728 (t) cc_final: 0.8348 (m) REVERT: F 166 ARG cc_start: 0.8600 (mtp85) cc_final: 0.7894 (ttp80) REVERT: N 47 MET cc_start: 0.8626 (mmm) cc_final: 0.8379 (mmm) REVERT: N 61 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7696 (mtm110) REVERT: I 616 ASN cc_start: 0.8859 (p0) cc_final: 0.8558 (p0) REVERT: I 624 ASP cc_start: 0.9105 (m-30) cc_final: 0.8745 (m-30) REVERT: P 22 CYS cc_start: 0.7686 (t) cc_final: 0.7384 (t) REVERT: P 39 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: P 66 ARG cc_start: 0.7044 (ttp-170) cc_final: 0.6820 (ttp80) REVERT: R 54 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7536 (ttm110) outliers start: 51 outliers final: 45 residues processed: 380 average time/residue: 0.3638 time to fit residues: 219.6862 Evaluate side-chains 389 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 341 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 103 GLN 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 375 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 31 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 H residue 11 VAL Chi-restraints excluded: chain H residue 92 CYS 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 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 76 ASN Chi-restraints excluded: chain M residue 27 ASP 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 48 VAL 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 39 GLN Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 48 ILE 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: 0.6980 chunk 170 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** L 38 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116183 restraints weight = 30595.688| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.31 r_work: 0.3225 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3512 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= 0.144 Angle : 0.553 16.469 34572 Z= 0.275 Chirality : 0.045 0.480 3963 Planarity : 0.004 0.036 4299 Dihedral : 5.138 53.290 4614 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.89 % Allowed : 10.75 % Favored : 87.36 % 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: 0.94 (0.16), residues: 2994 helix: 2.06 (0.26), residues: 411 sheet: 0.96 (0.17), residues: 858 loop : 0.17 (0.16), residues: 1725 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 0.014 0.001 PHE C 67 TYR 0.015 0.001 TYR D 49 ARG 0.004 0.000 ARG O 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 51) link_NAG-ASN : angle 2.91553 ( 153) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.33031 ( 36) hydrogen bonds : bond 0.03542 ( 723) hydrogen bonds : angle 4.35782 ( 1872) SS BOND : bond 0.00460 ( 48) SS BOND : angle 1.41935 ( 96) covalent geometry : bond 0.00344 (25281) covalent geometry : angle 0.51320 (34287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17525.60 seconds wall clock time: 308 minutes 45.95 seconds (18525.95 seconds total)