Starting phenix.real_space_refine on Sun Oct 12 13:09:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4d_41027/10_2025/8t4d_41027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4d_41027/10_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_41027/10_2025/8t4d_41027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4d_41027/10_2025/8t4d_41027.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4d_41027/10_2025/8t4d_41027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4d_41027/10_2025/8t4d_41027.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 6.19, per 1000 atoms: 0.25 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.06 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: 5.06 Time building geometry restraints manager: 2.90 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: 0.07 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (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 ARG 0.014 0.001 ARG A 500 TYR 0.023 0.003 TYR O 98 PHE 0.024 0.003 PHE P 100B TRP 0.020 0.003 TRP B 614 HIS 0.006 0.002 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00611 (25281) covalent geometry : angle 1.01112 (34287) SS BOND : bond 0.00701 ( 48) SS BOND : angle 1.93770 ( 96) hydrogen bonds : bond 0.13115 ( 723) hydrogen bonds : angle 6.36432 ( 1872) link_BETA1-4 : bond 0.00377 ( 12) link_BETA1-4 : angle 1.28251 ( 36) link_NAG-ASN : bond 0.00374 ( 51) link_NAG-ASN : angle 2.82342 ( 153) *********************** 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 : 1.023 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: 0.7717 (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: 0.7452 (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: 0.8275 (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: 0.1823 time to fit residues: 169.0717 Evaluate side-chains 398 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 374 HIS D 95 GLN B 577 GLN B 630 GLN B 637 ASN H 39 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS J 100BGLN M 95 GLN O 39 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS F 428 GLN N 95 GLN I 637 ASN P 39 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121150 restraints weight = 30401.708| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.45 r_work: 0.3257 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25392 Z= 0.215 Angle : 0.677 14.386 34572 Z= 0.345 Chirality : 0.050 0.537 3963 Planarity : 0.005 0.039 4299 Dihedral : 7.232 58.995 4618 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.42 % Allowed : 5.86 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.15), residues: 2994 helix: 1.78 (0.27), residues: 411 sheet: 1.29 (0.16), residues: 900 loop : 0.50 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 94 TYR 0.024 0.002 TYR H 98 PHE 0.016 0.002 PHE A 383 TRP 0.013 0.002 TRP Q 35 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00510 (25281) covalent geometry : angle 0.64402 (34287) SS BOND : bond 0.00588 ( 48) SS BOND : angle 1.38933 ( 96) hydrogen bonds : bond 0.04584 ( 723) hydrogen bonds : angle 5.12273 ( 1872) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.77149 ( 36) link_NAG-ASN : bond 0.00412 ( 51) link_NAG-ASN : angle 2.92796 ( 153) *********************** 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 465 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 401 time to evaluate : 0.911 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 123 THR cc_start: 0.9155 (m) cc_final: 0.8934 (p) REVERT: A 166 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7769 (mtm110) REVERT: C 66 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7408 (mtm110) REVERT: B 616 ASN cc_start: 0.8734 (p0) cc_final: 0.8462 (p0) REVERT: H 39 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: L 54 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7663 (ttm110) REVERT: E 110 SER cc_start: 0.8629 (t) cc_final: 0.8267 (m) REVERT: E 123 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8976 (p) REVERT: E 150 MET cc_start: 0.8928 (mtp) cc_final: 0.8718 (mtm) REVERT: E 166 ARG cc_start: 0.8491 (mtp85) cc_final: 0.7698 (ttp80) REVERT: M 47 MET cc_start: 0.8825 (mmm) cc_final: 0.8574 (mmt) REVERT: O 39 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: O 77 THR cc_start: 0.8687 (m) cc_final: 0.8326 (p) REVERT: O 105 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7629 (ptp90) REVERT: Q 33 LEU cc_start: 0.8761 (tp) cc_final: 0.8525 (tp) REVERT: Q 54 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7377 (ttm110) REVERT: F 110 SER cc_start: 0.8726 (t) cc_final: 0.8366 (m) REVERT: F 166 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7718 (mtm110) REVERT: F 199 SER cc_start: 0.9024 (p) cc_final: 0.8661 (p) REVERT: F 269 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7775 (pt0) REVERT: K 56 LEU cc_start: 0.8898 (mt) cc_final: 0.8692 (mt) REVERT: K 72 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: N 47 MET cc_start: 0.8738 (mmm) cc_final: 0.8505 (mmt) REVERT: I 624 ASP cc_start: 0.9013 (m-30) cc_final: 0.8749 (m-30) REVERT: P 66 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7175 (ttp80) REVERT: P 105 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7597 (ptp90) REVERT: R 53 ASN cc_start: 0.7843 (t0) cc_final: 0.7491 (m-40) outliers start: 64 outliers final: 42 residues processed: 444 average time/residue: 0.1812 time to fit residues: 125.6750 Evaluate side-chains 409 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 GLN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 65 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 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 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 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 146 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 210 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 277 optimal weight: 0.6980 chunk 186 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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** G 637 ASN O 39 GLN F 195 ASN N 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.159984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124421 restraints weight = 30407.934| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.26 r_work: 0.3306 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2276 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= 0.118 Angle : 0.557 10.109 34572 Z= 0.284 Chirality : 0.045 0.500 3963 Planarity : 0.004 0.038 4299 Dihedral : 6.008 52.667 4614 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.63 % Allowed : 7.83 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.15), residues: 2994 helix: 2.08 (0.27), residues: 411 sheet: 1.43 (0.17), residues: 864 loop : 0.45 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.013 0.001 TYR H 98 PHE 0.017 0.001 PHE H 100B TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00264 (25281) covalent geometry : angle 0.52874 (34287) SS BOND : bond 0.00437 ( 48) SS BOND : angle 0.98757 ( 96) hydrogen bonds : bond 0.03761 ( 723) hydrogen bonds : angle 4.76710 ( 1872) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.44500 ( 36) link_NAG-ASN : bond 0.00407 ( 51) link_NAG-ASN : angle 2.51058 ( 153) *********************** 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 442 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 399 time to evaluate : 0.958 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: 0.8568 (tttm) cc_final: 0.8226 (mttm) REVERT: A 123 THR cc_start: 0.9129 (m) cc_final: 0.8892 (p) REVERT: A 166 ARG cc_start: 0.8496 (mtp85) cc_final: 0.7832 (mtm110) REVERT: C 18 LEU cc_start: 0.8391 (tp) cc_final: 0.8176 (tp) REVERT: C 66 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7474 (mtm110) REVERT: B 616 ASN cc_start: 0.8719 (p0) cc_final: 0.8449 (p0) REVERT: H 77 THR cc_start: 0.8680 (m) cc_final: 0.8353 (p) REVERT: H 105 ARG cc_start: 0.8005 (ptp90) cc_final: 0.7781 (ptp90) REVERT: L 28 ASP cc_start: 0.8697 (m-30) cc_final: 0.8224 (m-30) REVERT: L 54 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7664 (ttm110) REVERT: E 110 SER cc_start: 0.8581 (t) cc_final: 0.8236 (m) REVERT: E 123 THR cc_start: 0.9170 (m) cc_final: 0.8967 (p) REVERT: E 150 MET cc_start: 0.8878 (mtp) cc_final: 0.8631 (mtm) REVERT: E 166 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7654 (ttp80) REVERT: E 269 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7739 (pt0) REVERT: O 77 THR cc_start: 0.8598 (m) cc_final: 0.8395 (p) REVERT: Q 31 THR cc_start: 0.8438 (m) cc_final: 0.7882 (p) REVERT: Q 33 LEU cc_start: 0.8798 (tp) cc_final: 0.8548 (tp) REVERT: Q 54 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7528 (ttm110) REVERT: F 110 SER cc_start: 0.8621 (t) cc_final: 0.8234 (m) REVERT: F 111 LEU cc_start: 0.8510 (mp) cc_final: 0.8285 (mp) REVERT: F 114 GLN cc_start: 0.8234 (mt0) cc_final: 0.7929 (tt0) REVERT: F 166 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7760 (mtm110) REVERT: F 199 SER cc_start: 0.9013 (p) cc_final: 0.8747 (p) REVERT: K 56 LEU cc_start: 0.8921 (mt) cc_final: 0.8720 (mt) REVERT: N 47 MET cc_start: 0.8670 (mmm) cc_final: 0.8406 (mmt) REVERT: I 624 ASP cc_start: 0.9053 (m-30) cc_final: 0.8724 (m-30) REVERT: P 105 ARG cc_start: 0.7762 (ptp90) cc_final: 0.7513 (ptp90) REVERT: R 54 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7252 (ttm110) outliers start: 43 outliers final: 25 residues processed: 425 average time/residue: 0.1773 time to fit residues: 118.0702 Evaluate side-chains 391 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 366 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU 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 211 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 284 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS C 39 GLN D 39 HIS H 39 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 HIS M 39 HIS O 39 GLN F 195 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 = 0.3803 r_free = 0.3803 target = 0.152919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116329 restraints weight = 30693.449| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.35 r_work: 0.3203 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25392 Z= 0.256 Angle : 0.650 13.384 34572 Z= 0.327 Chirality : 0.048 0.472 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.853 53.379 4614 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.15), residues: 2994 helix: 1.67 (0.26), residues: 411 sheet: 0.93 (0.17), residues: 918 loop : 0.37 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 61 TYR 0.014 0.002 TYR A 319 PHE 0.018 0.002 PHE E 317 TRP 0.013 0.002 TRP A 96 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00628 (25281) covalent geometry : angle 0.61648 (34287) SS BOND : bond 0.00529 ( 48) SS BOND : angle 1.24259 ( 96) hydrogen bonds : bond 0.04430 ( 723) hydrogen bonds : angle 4.81097 ( 1872) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.56572 ( 36) link_NAG-ASN : bond 0.00428 ( 51) link_NAG-ASN : angle 2.94072 ( 153) *********************** 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 421 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 0.992 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: 0.8586 (tttm) cc_final: 0.8242 (mttm) REVERT: A 166 ARG cc_start: 0.8528 (mtp85) cc_final: 0.7738 (ttp80) REVERT: B 616 ASN cc_start: 0.8779 (p0) cc_final: 0.8417 (p0) REVERT: H 80 MET cc_start: 0.7792 (ttp) cc_final: 0.7417 (ttp) REVERT: L 28 ASP cc_start: 0.8810 (m-30) cc_final: 0.8388 (m-30) REVERT: L 54 ARG cc_start: 0.8008 (ttm110) cc_final: 0.7682 (ttm110) REVERT: E 110 SER cc_start: 0.8699 (t) cc_final: 0.8260 (m) REVERT: E 166 ARG cc_start: 0.8522 (mtp85) cc_final: 0.7758 (ttp80) REVERT: E 269 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7795 (pt0) REVERT: E 358 ILE cc_start: 0.7874 (mt) cc_final: 0.7538 (mm) REVERT: Q 54 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7675 (ttm110) REVERT: F 110 SER cc_start: 0.8768 (t) cc_final: 0.8409 (m) REVERT: F 111 LEU cc_start: 0.8629 (mp) cc_final: 0.8355 (mp) REVERT: F 166 ARG cc_start: 0.8570 (mtp85) cc_final: 0.7894 (ttp80) REVERT: F 199 SER cc_start: 0.9038 (p) cc_final: 0.8790 (p) REVERT: F 358 ILE cc_start: 0.7760 (mt) cc_final: 0.7452 (mm) REVERT: K 80 LEU cc_start: 0.7774 (tt) cc_final: 0.7564 (tp) REVERT: N 47 MET cc_start: 0.8694 (mmm) cc_final: 0.8449 (mmm) REVERT: I 616 ASN cc_start: 0.8852 (p0) cc_final: 0.8613 (p0) REVERT: I 624 ASP cc_start: 0.8997 (m-30) cc_final: 0.8694 (m-30) REVERT: R 54 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7379 (ttm110) outliers start: 55 outliers final: 45 residues processed: 403 average time/residue: 0.1759 time to fit residues: 111.9193 Evaluate side-chains 395 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 116 LEU 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 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 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 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 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 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 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 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 48 ILE 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 195 optimal weight: 0.7980 chunk 233 optimal weight: 0.0270 chunk 264 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 186 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 151 optimal weight: 0.0570 chunk 185 optimal weight: 0.7980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN B 637 ASN H 39 GLN H 100KASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN M 95 GLN G 637 ASN O 100KASN F 195 ASN N 95 GLN I 607 ASN I 652 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120533 restraints weight = 30390.893| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.45 r_work: 0.3238 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25392 Z= 0.101 Angle : 0.526 11.761 34572 Z= 0.266 Chirality : 0.044 0.442 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.288 52.783 4614 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.59 % Allowed : 9.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.16), residues: 2994 helix: 2.07 (0.26), residues: 411 sheet: 1.01 (0.17), residues: 912 loop : 0.43 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 500 TYR 0.014 0.001 TYR D 49 PHE 0.010 0.001 PHE R 96 TRP 0.015 0.001 TRP H 50 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00225 (25281) covalent geometry : angle 0.49685 (34287) SS BOND : bond 0.00418 ( 48) SS BOND : angle 0.97773 ( 96) hydrogen bonds : bond 0.03375 ( 723) hydrogen bonds : angle 4.53369 ( 1872) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 1.23464 ( 36) link_NAG-ASN : bond 0.00456 ( 51) link_NAG-ASN : angle 2.47914 ( 153) *********************** 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 421 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8496 (tttm) cc_final: 0.8144 (mttm) REVERT: A 166 ARG cc_start: 0.8565 (mtp85) cc_final: 0.7667 (ttp80) REVERT: A 475 MET cc_start: 0.8344 (mmt) cc_final: 0.8051 (mmt) REVERT: C 66 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7503 (mtp180) REVERT: B 616 ASN cc_start: 0.8762 (p0) cc_final: 0.8488 (p0) REVERT: H 22 CYS cc_start: 0.7697 (t) cc_final: 0.7454 (t) REVERT: H 80 MET cc_start: 0.7747 (ttp) cc_final: 0.7519 (ttp) REVERT: L 4 MET cc_start: 0.7465 (mpp) cc_final: 0.7173 (mpp) REVERT: L 28 ASP cc_start: 0.8769 (m-30) cc_final: 0.8356 (m-30) REVERT: L 54 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7704 (ttm110) REVERT: L 89 MET cc_start: 0.8252 (tpp) cc_final: 0.7925 (ttp) REVERT: E 110 SER cc_start: 0.8617 (t) cc_final: 0.8185 (m) REVERT: E 166 ARG cc_start: 0.8559 (mtp85) cc_final: 0.7649 (ttp80) REVERT: E 358 ILE cc_start: 0.7771 (mt) cc_final: 0.7431 (mm) REVERT: Q 28 ASP cc_start: 0.8638 (m-30) cc_final: 0.8413 (m-30) REVERT: Q 33 LEU cc_start: 0.8804 (tp) cc_final: 0.8541 (tp) REVERT: Q 54 ARG cc_start: 0.7979 (ttm110) cc_final: 0.7560 (ttm110) REVERT: F 106 GLU cc_start: 0.8185 (mp0) cc_final: 0.7902 (mp0) REVERT: F 110 SER cc_start: 0.8613 (t) cc_final: 0.8238 (m) REVERT: F 111 LEU cc_start: 0.8582 (mp) cc_final: 0.8350 (mp) REVERT: F 114 GLN cc_start: 0.8221 (mt0) cc_final: 0.7886 (tt0) REVERT: F 166 ARG cc_start: 0.8591 (mtp85) cc_final: 0.7753 (ttp80) REVERT: K 80 LEU cc_start: 0.7621 (tt) cc_final: 0.7361 (tp) REVERT: N 47 MET cc_start: 0.8669 (mmm) cc_final: 0.8417 (mmt) REVERT: N 61 ARG cc_start: 0.8006 (mtm110) cc_final: 0.7569 (mtm110) REVERT: I 616 ASN cc_start: 0.8769 (p0) cc_final: 0.8510 (p0) REVERT: I 624 ASP cc_start: 0.9102 (m-30) cc_final: 0.8790 (m-30) REVERT: P 22 CYS cc_start: 0.7647 (t) cc_final: 0.7330 (t) REVERT: P 77 THR cc_start: 0.8580 (m) cc_final: 0.8270 (p) REVERT: R 54 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7367 (ttm110) outliers start: 42 outliers final: 26 residues processed: 408 average time/residue: 0.1697 time to fit residues: 110.3861 Evaluate side-chains 378 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 195 ASN 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 48 VAL Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain P residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 283 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 89 optimal weight: 0.0050 chunk 216 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 95 GLN B 637 ASN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS G 637 ASN O 100KASN F 195 ASN N 95 GLN I 652 GLN P 39 GLN R 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117991 restraints weight = 30461.361| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.43 r_work: 0.3210 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3012 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= 0.150 Angle : 0.554 16.242 34572 Z= 0.276 Chirality : 0.045 0.446 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.200 52.906 4614 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.70 % Allowed : 9.88 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.16), residues: 2994 helix: 2.04 (0.26), residues: 411 sheet: 0.95 (0.17), residues: 909 loop : 0.31 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 66 TYR 0.012 0.001 TYR D 49 PHE 0.011 0.001 PHE J 67 TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (25281) covalent geometry : angle 0.51685 (34287) SS BOND : bond 0.00501 ( 48) SS BOND : angle 1.01864 ( 96) hydrogen bonds : bond 0.03634 ( 723) hydrogen bonds : angle 4.50589 ( 1872) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.31990 ( 36) link_NAG-ASN : bond 0.00444 ( 51) link_NAG-ASN : angle 2.88764 ( 153) *********************** 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 403 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8498 (tttm) cc_final: 0.8177 (mttm) REVERT: A 166 ARG cc_start: 0.8591 (mtp85) cc_final: 0.7717 (ttp80) REVERT: B 616 ASN cc_start: 0.8755 (p0) cc_final: 0.8505 (p0) REVERT: H 22 CYS cc_start: 0.7717 (t) cc_final: 0.7477 (t) REVERT: H 80 MET cc_start: 0.7760 (ttp) cc_final: 0.7479 (ttp) REVERT: L 4 MET cc_start: 0.7453 (mpp) cc_final: 0.7129 (mpp) REVERT: L 28 ASP cc_start: 0.8797 (m-30) cc_final: 0.8375 (m-30) REVERT: L 54 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7730 (ttm110) REVERT: E 110 SER cc_start: 0.8655 (t) cc_final: 0.8217 (m) REVERT: E 166 ARG cc_start: 0.8615 (mtp85) cc_final: 0.7756 (ttp80) REVERT: E 358 ILE cc_start: 0.7869 (mt) cc_final: 0.7546 (mm) REVERT: G 616 ASN cc_start: 0.8861 (p0) cc_final: 0.8364 (p0) REVERT: Q 31 THR cc_start: 0.8480 (m) cc_final: 0.7972 (p) REVERT: Q 33 LEU cc_start: 0.8783 (tp) cc_final: 0.8520 (tp) REVERT: Q 54 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7551 (ttm110) REVERT: F 106 GLU cc_start: 0.8194 (mp0) cc_final: 0.7882 (mp0) REVERT: F 110 SER cc_start: 0.8745 (t) cc_final: 0.8386 (m) REVERT: F 111 LEU cc_start: 0.8631 (mp) cc_final: 0.8387 (mp) REVERT: F 166 ARG cc_start: 0.8601 (mtp85) cc_final: 0.7826 (ttp80) REVERT: K 80 LEU cc_start: 0.7720 (tt) cc_final: 0.7501 (tp) REVERT: N 47 MET cc_start: 0.8671 (mmm) cc_final: 0.8444 (mmm) REVERT: N 61 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7691 (mtm110) REVERT: I 616 ASN cc_start: 0.8795 (p0) cc_final: 0.8507 (p0) REVERT: I 624 ASP cc_start: 0.9088 (m-30) cc_final: 0.8771 (m-30) REVERT: P 22 CYS cc_start: 0.7744 (t) cc_final: 0.7437 (t) REVERT: P 39 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: R 54 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7411 (ttm110) outliers start: 45 outliers final: 30 residues processed: 387 average time/residue: 0.1730 time to fit residues: 105.6945 Evaluate side-chains 376 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 345 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 325 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 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 39 GLN Chi-restraints excluded: chain P residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 222 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 95 GLN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 637 ASN I 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114072 restraints weight = 30455.581| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.22 r_work: 0.3192 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25392 Z= 0.187 Angle : 0.578 17.605 34572 Z= 0.288 Chirality : 0.046 0.565 3963 Planarity : 0.004 0.038 4299 Dihedral : 5.274 53.216 4614 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 9.84 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 2994 helix: 1.94 (0.26), residues: 411 sheet: 0.89 (0.17), residues: 903 loop : 0.23 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 66 TYR 0.012 0.001 TYR D 49 PHE 0.013 0.002 PHE E 383 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00454 (25281) covalent geometry : angle 0.54018 (34287) SS BOND : bond 0.00464 ( 48) SS BOND : angle 1.09323 ( 96) hydrogen bonds : bond 0.03857 ( 723) hydrogen bonds : angle 4.54689 ( 1872) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.37003 ( 36) link_NAG-ASN : bond 0.00448 ( 51) link_NAG-ASN : angle 2.99647 ( 153) *********************** 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 398 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8442 (tttm) cc_final: 0.8119 (mttm) REVERT: A 166 ARG cc_start: 0.8557 (mtp85) cc_final: 0.7754 (ttp80) REVERT: B 616 ASN cc_start: 0.8764 (p0) cc_final: 0.8421 (p0) REVERT: H 22 CYS cc_start: 0.7804 (t) cc_final: 0.7572 (t) REVERT: H 80 MET cc_start: 0.7748 (ttp) cc_final: 0.7503 (ttp) REVERT: L 4 MET cc_start: 0.7521 (mpp) cc_final: 0.7192 (mpp) REVERT: L 28 ASP cc_start: 0.8836 (m-30) cc_final: 0.8422 (m-30) REVERT: E 110 SER cc_start: 0.8667 (t) cc_final: 0.8218 (m) REVERT: E 166 ARG cc_start: 0.8621 (mtp85) cc_final: 0.7717 (ttp80) REVERT: E 246 GLN cc_start: 0.7851 (tp40) cc_final: 0.7632 (mp10) REVERT: E 358 ILE cc_start: 0.7931 (mt) cc_final: 0.7609 (mm) REVERT: J 31 SER cc_start: 0.9110 (t) cc_final: 0.8869 (t) REVERT: G 616 ASN cc_start: 0.8923 (p0) cc_final: 0.8431 (p0) REVERT: Q 31 THR cc_start: 0.8494 (m) cc_final: 0.7958 (p) REVERT: Q 33 LEU cc_start: 0.8825 (tp) cc_final: 0.8547 (tp) REVERT: Q 54 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7666 (ttm110) REVERT: F 106 GLU cc_start: 0.8157 (mp0) cc_final: 0.7842 (mp0) REVERT: F 110 SER cc_start: 0.8797 (t) cc_final: 0.8441 (m) REVERT: F 111 LEU cc_start: 0.8635 (mp) cc_final: 0.8388 (mp) REVERT: F 166 ARG cc_start: 0.8645 (mtp85) cc_final: 0.7885 (ttp80) REVERT: N 47 MET cc_start: 0.8666 (mmm) cc_final: 0.8423 (mmm) REVERT: N 61 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7777 (mtm110) REVERT: I 616 ASN cc_start: 0.8832 (p0) cc_final: 0.8528 (p0) REVERT: I 624 ASP cc_start: 0.9132 (m-30) cc_final: 0.8805 (m-30) REVERT: P 22 CYS cc_start: 0.7786 (t) cc_final: 0.7488 (t) REVERT: R 54 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7499 (ttm110) outliers start: 53 outliers final: 42 residues processed: 381 average time/residue: 0.1712 time to fit residues: 103.2764 Evaluate side-chains 378 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 43 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain 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 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 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 75 THR 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 124 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 291 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 193 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 95 GLN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN N 95 GLN P 39 GLN P 100KASN R 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118421 restraints weight = 30449.167| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.34 r_work: 0.3222 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25392 Z= 0.146 Angle : 0.553 16.288 34572 Z= 0.275 Chirality : 0.044 0.473 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.224 53.123 4614 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.01 % Allowed : 9.88 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 2994 helix: 2.01 (0.26), residues: 411 sheet: 0.87 (0.17), residues: 903 loop : 0.21 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.014 0.001 TYR D 49 PHE 0.010 0.001 PHE J 67 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00349 (25281) covalent geometry : angle 0.51628 (34287) SS BOND : bond 0.00462 ( 48) SS BOND : angle 1.14386 ( 96) hydrogen bonds : bond 0.03624 ( 723) hydrogen bonds : angle 4.48380 ( 1872) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 1.30538 ( 36) link_NAG-ASN : bond 0.00545 ( 51) link_NAG-ASN : angle 2.84067 ( 153) *********************** 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 395 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8483 (tttm) cc_final: 0.8102 (mttm) REVERT: A 166 ARG cc_start: 0.8529 (mtp85) cc_final: 0.7681 (ttp80) REVERT: D 61 ARG cc_start: 0.8231 (mtm110) cc_final: 0.7972 (mtm110) REVERT: B 616 ASN cc_start: 0.8749 (p0) cc_final: 0.8406 (p0) REVERT: H 22 CYS cc_start: 0.7693 (t) cc_final: 0.7452 (t) REVERT: H 80 MET cc_start: 0.7740 (ttp) cc_final: 0.7504 (ttp) REVERT: L 31 THR cc_start: 0.8474 (m) cc_final: 0.8013 (p) REVERT: E 51 THR cc_start: 0.8984 (m) cc_final: 0.8728 (p) REVERT: E 110 SER cc_start: 0.8657 (t) cc_final: 0.8204 (m) REVERT: E 166 ARG cc_start: 0.8552 (mtp85) cc_final: 0.7745 (ttp80) REVERT: E 358 ILE cc_start: 0.7937 (mt) cc_final: 0.7622 (mm) REVERT: E 432 GLN cc_start: 0.8564 (mt0) cc_final: 0.8295 (mt0) REVERT: J 31 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8871 (t) REVERT: M 61 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7616 (mtm110) REVERT: G 616 ASN cc_start: 0.8896 (p0) cc_final: 0.8455 (p0) REVERT: G 624 ASP cc_start: 0.8953 (m-30) cc_final: 0.8750 (m-30) REVERT: O 90 TYR cc_start: 0.8071 (m-80) cc_final: 0.7823 (m-80) REVERT: Q 28 ASP cc_start: 0.8683 (m-30) cc_final: 0.8476 (m-30) REVERT: Q 54 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7662 (ttm110) REVERT: F 106 GLU cc_start: 0.8131 (mp0) cc_final: 0.7824 (mp0) REVERT: F 110 SER cc_start: 0.8785 (t) cc_final: 0.8448 (m) REVERT: F 111 LEU cc_start: 0.8635 (mp) cc_final: 0.8388 (mp) REVERT: F 166 ARG cc_start: 0.8592 (mtp85) cc_final: 0.7884 (ttp80) REVERT: F 358 ILE cc_start: 0.7753 (mt) cc_final: 0.7472 (mm) REVERT: N 47 MET cc_start: 0.8633 (mmm) cc_final: 0.8403 (mmm) REVERT: N 61 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7694 (mtm110) REVERT: I 616 ASN cc_start: 0.8724 (p0) cc_final: 0.8423 (p0) REVERT: I 624 ASP cc_start: 0.9099 (m-30) cc_final: 0.8749 (m-30) REVERT: P 22 CYS cc_start: 0.7670 (t) cc_final: 0.7380 (t) REVERT: P 66 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6628 (ttt180) REVERT: R 54 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7447 (ttm110) outliers start: 53 outliers final: 43 residues processed: 378 average time/residue: 0.1714 time to fit residues: 103.2753 Evaluate side-chains 381 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 325 HIS Chi-restraints excluded: chain E residue 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN M 95 GLN G 637 ASN N 95 GLN P 39 GLN P 100KASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115321 restraints weight = 30486.798| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.22 r_work: 0.3201 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25392 Z= 0.140 Angle : 0.553 16.669 34572 Z= 0.274 Chirality : 0.045 0.516 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.150 53.128 4614 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.93 % Allowed : 10.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2994 helix: 2.06 (0.26), residues: 411 sheet: 0.97 (0.17), residues: 882 loop : 0.16 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.014 0.001 TYR D 49 PHE 0.011 0.001 PHE A 383 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00334 (25281) covalent geometry : angle 0.51118 (34287) SS BOND : bond 0.00463 ( 48) SS BOND : angle 1.25698 ( 96) hydrogen bonds : bond 0.03561 ( 723) hydrogen bonds : angle 4.42860 ( 1872) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.30998 ( 36) link_NAG-ASN : bond 0.00594 ( 51) link_NAG-ASN : angle 3.00619 ( 153) *********************** 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 391 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8473 (tttm) cc_final: 0.8089 (mttm) REVERT: A 166 ARG cc_start: 0.8565 (mtp85) cc_final: 0.7735 (ttp80) REVERT: A 396 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (tp) REVERT: D 61 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7989 (mtm110) REVERT: B 616 ASN cc_start: 0.8787 (p0) cc_final: 0.8445 (p0) REVERT: H 22 CYS cc_start: 0.7650 (t) cc_final: 0.7402 (t) REVERT: H 80 MET cc_start: 0.7761 (ttp) cc_final: 0.7521 (ttp) REVERT: L 31 THR cc_start: 0.8496 (m) cc_final: 0.8055 (p) REVERT: E 51 THR cc_start: 0.8926 (m) cc_final: 0.8678 (p) REVERT: E 110 SER cc_start: 0.8665 (t) cc_final: 0.8215 (m) REVERT: E 166 ARG cc_start: 0.8558 (mtp85) cc_final: 0.7722 (ttp80) REVERT: E 358 ILE cc_start: 0.7952 (mt) cc_final: 0.7633 (mm) REVERT: E 432 GLN cc_start: 0.8584 (mt0) cc_final: 0.8294 (mt0) REVERT: J 31 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (t) REVERT: M 61 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7626 (mtm110) REVERT: G 616 ASN cc_start: 0.8918 (p0) cc_final: 0.8474 (p0) REVERT: G 624 ASP cc_start: 0.8934 (m-30) cc_final: 0.8729 (m-30) REVERT: Q 28 ASP cc_start: 0.8687 (m-30) cc_final: 0.8480 (m-30) REVERT: Q 54 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7655 (ttm110) REVERT: F 106 GLU cc_start: 0.8133 (mp0) cc_final: 0.7823 (mp0) REVERT: F 110 SER cc_start: 0.8790 (t) cc_final: 0.8449 (m) REVERT: F 111 LEU cc_start: 0.8637 (mp) cc_final: 0.8371 (mp) REVERT: F 166 ARG cc_start: 0.8603 (mtp85) cc_final: 0.7883 (ttp80) REVERT: F 358 ILE cc_start: 0.7778 (mt) cc_final: 0.7491 (mm) REVERT: K 27 TYR cc_start: 0.8124 (p90) cc_final: 0.7879 (p90) REVERT: K 102 PHE cc_start: 0.8601 (m-80) cc_final: 0.8378 (m-10) REVERT: N 47 MET cc_start: 0.8636 (mmm) cc_final: 0.8392 (mmm) REVERT: N 61 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7968 (mtm110) REVERT: I 616 ASN cc_start: 0.8737 (p0) cc_final: 0.8433 (p0) REVERT: I 624 ASP cc_start: 0.9110 (m-30) cc_final: 0.8751 (m-30) REVERT: P 22 CYS cc_start: 0.7694 (t) cc_final: 0.7380 (t) REVERT: P 66 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6677 (ttt180) REVERT: R 54 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7484 (ttm110) outliers start: 51 outliers final: 42 residues processed: 376 average time/residue: 0.1739 time to fit residues: 103.4184 Evaluate side-chains 380 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 43 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 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 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 20 SER Chi-restraints excluded: chain R residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 282 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118073 restraints weight = 30612.241| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.29 r_work: 0.3222 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3385 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= 0.138 Angle : 0.549 15.981 34572 Z= 0.273 Chirality : 0.045 0.517 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.111 53.156 4614 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.93 % Allowed : 10.56 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2994 helix: 2.10 (0.26), residues: 411 sheet: 0.96 (0.17), residues: 882 loop : 0.15 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.015 0.001 TYR D 49 PHE 0.010 0.001 PHE C 67 TRP 0.013 0.001 TRP H 50 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00328 (25281) covalent geometry : angle 0.50881 (34287) SS BOND : bond 0.00434 ( 48) SS BOND : angle 1.20650 ( 96) hydrogen bonds : bond 0.03522 ( 723) hydrogen bonds : angle 4.38736 ( 1872) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.30766 ( 36) link_NAG-ASN : bond 0.00573 ( 51) link_NAG-ASN : angle 2.94509 ( 153) ********************** 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 391 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8462 (tttm) cc_final: 0.8133 (mttm) REVERT: A 166 ARG cc_start: 0.8569 (mtp85) cc_final: 0.7820 (ttp80) REVERT: A 432 GLN cc_start: 0.8439 (mt0) cc_final: 0.8195 (mt0) REVERT: D 61 ARG cc_start: 0.8264 (mtm110) cc_final: 0.8000 (mtm110) REVERT: B 616 ASN cc_start: 0.8819 (p0) cc_final: 0.8447 (p0) REVERT: H 22 CYS cc_start: 0.7702 (t) cc_final: 0.7481 (t) REVERT: L 4 MET cc_start: 0.7453 (mpp) cc_final: 0.7188 (mpp) REVERT: L 31 THR cc_start: 0.8477 (m) cc_final: 0.8063 (p) REVERT: E 51 THR cc_start: 0.8930 (m) cc_final: 0.8714 (p) REVERT: E 82 GLN cc_start: 0.7092 (tt0) cc_final: 0.6795 (tt0) REVERT: E 110 SER cc_start: 0.8669 (t) cc_final: 0.8221 (m) REVERT: E 166 ARG cc_start: 0.8547 (mtp85) cc_final: 0.7634 (ttp80) REVERT: E 358 ILE cc_start: 0.7962 (mt) cc_final: 0.7654 (mm) REVERT: E 432 GLN cc_start: 0.8544 (mt0) cc_final: 0.8239 (mt0) REVERT: J 31 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8881 (t) REVERT: M 61 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7813 (mtm110) REVERT: G 616 ASN cc_start: 0.8876 (p0) cc_final: 0.8440 (p0) REVERT: G 624 ASP cc_start: 0.8943 (m-30) cc_final: 0.8738 (m-30) REVERT: Q 28 ASP cc_start: 0.8690 (m-30) cc_final: 0.8485 (m-30) REVERT: F 106 GLU cc_start: 0.8134 (mp0) cc_final: 0.7830 (mp0) REVERT: F 110 SER cc_start: 0.8785 (t) cc_final: 0.8447 (m) REVERT: F 111 LEU cc_start: 0.8638 (mp) cc_final: 0.8372 (mp) REVERT: F 166 ARG cc_start: 0.8651 (mtp85) cc_final: 0.7811 (ttp80) REVERT: F 358 ILE cc_start: 0.7791 (mt) cc_final: 0.7512 (mm) REVERT: N 47 MET cc_start: 0.8595 (mmm) cc_final: 0.8361 (mmm) REVERT: N 61 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7657 (mtm110) REVERT: I 616 ASN cc_start: 0.8774 (p0) cc_final: 0.8467 (p0) REVERT: I 624 ASP cc_start: 0.9113 (m-30) cc_final: 0.8755 (m-30) REVERT: P 22 CYS cc_start: 0.7639 (t) cc_final: 0.7325 (t) REVERT: P 66 ARG cc_start: 0.7135 (ttt180) cc_final: 0.6740 (ttt180) REVERT: R 54 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7511 (ttm110) outliers start: 51 outliers final: 44 residues processed: 378 average time/residue: 0.1736 time to fit residues: 104.1284 Evaluate side-chains 379 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 43 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 375 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 325 HIS Chi-restraints excluded: chain F residue 375 SER Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain K residue 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 75 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 92 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 289 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 286 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN L 38 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN G 637 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN I 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117414 restraints weight = 30654.244| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.30 r_work: 0.3234 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25392 Z= 0.152 Angle : 0.553 16.073 34572 Z= 0.275 Chirality : 0.045 0.517 3963 Planarity : 0.004 0.037 4299 Dihedral : 5.127 53.278 4614 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.89 % Allowed : 10.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.16), residues: 2994 helix: 2.06 (0.26), residues: 411 sheet: 0.84 (0.17), residues: 918 loop : 0.19 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.014 0.001 TYR D 49 PHE 0.011 0.001 PHE C 67 TRP 0.013 0.001 TRP H 50 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00366 (25281) covalent geometry : angle 0.51494 (34287) SS BOND : bond 0.00459 ( 48) SS BOND : angle 1.19872 ( 96) hydrogen bonds : bond 0.03588 ( 723) hydrogen bonds : angle 4.37736 ( 1872) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.33941 ( 36) link_NAG-ASN : bond 0.00614 ( 51) link_NAG-ASN : angle 2.91107 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7539.33 seconds wall clock time: 129 minutes 32.66 seconds (7772.66 seconds total)