Starting phenix.real_space_refine on Wed May 21 08:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfv_43190/05_2025/8vfv_43190.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 13320 2.51 5 N 3563 2.21 5 O 4224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 29 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 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: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "M" 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: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "K" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" 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 Time building chain proxies: 15.32, per 1000 atoms: 0.72 Number of scatterers: 21240 At special positions: 0 Unit cell: (141.984, 127.368, 171.216, 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 133 16.00 O 4224 8.00 N 3563 7.00 C 13320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 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=2.02 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 F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=1.99 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 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 B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.01 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.04 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.04 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 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 ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN R 4 " - " MAN R 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA O 3 " - " MAN O 6 " " BMA R 3 " - " MAN R 6 " " BMA U 3 " - " MAN U 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 156 " " 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 301 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 156 " " 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 301 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 133 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 234 " " NAG J 606 " - " ASN J 276 " " NAG J 607 " - " ASN J 295 " " NAG J 608 " - " ASN J 301 " " NAG J 609 " - " ASN J 448 " " NAG J 610 " - " ASN J 133 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 637 " " NAG O 1 " - " ASN E 332 " " NAG P 1 " - " ASN E 262 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN J 332 " " NAG V 1 " - " ASN J 262 " " NAG W 1 " - " ASN J 386 " Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 38 sheets defined 20.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.502A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.292A 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 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.805A 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 387 through 391 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.535A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.743A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.503A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.813A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.059A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.970A 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 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.404A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.655A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.377A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.680A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (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 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.725A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.430A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 195 through 198 Processing helix chain 'J' and resid 335 through 354 removed outlier: 3.709A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 391 Processing helix chain 'J' and resid 475 through 484 removed outlier: 3.547A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 536 through 543 removed outlier: 3.802A pdb=" N GLN K 540 " --> pdb=" O THR K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 596 Processing helix chain 'K' and resid 618 through 624 Processing helix chain 'K' and resid 627 through 636 Processing helix chain 'K' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 34 through 39 removed outlier: 6.978A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AA3, first strand: chain 'I' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 13 current: chain 'I' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 49 current: chain 'I' and resid 96 through 98 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.878A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB1, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.547A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB2, 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: 6.681A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.435A 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 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.999A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 102 through 103 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 13 current: chain 'D' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 96 through 98 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AC2, first strand: chain 'L' and resid 27C through 27D Processing sheet with id=AC3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.213A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.842A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC9, 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: 6.673A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.405A 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 470 Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'M' and resid 34 through 39 removed outlier: 6.983A pdb=" N MET M 34 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AD3, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AD5, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.113A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 45 through 47 Processing sheet with id=AD7, first strand: chain 'J' and resid 75 through 76 removed outlier: 5.600A pdb=" N ILE J 215 " --> pdb=" O GLY J 250 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY J 250 " --> pdb=" O ILE J 215 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR J 217 " --> pdb=" O THR J 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'J' and resid 169 through 176 Processing sheet with id=AE1, first strand: chain 'J' and resid 202 through 203 removed outlier: 6.574A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.619A pdb=" N ASN J 301 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE J 323 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323A current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 465 through 470 616 hydrogen bonds defined for protein. 1575 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: 7.35 Time building geometry restraints manager: 6.26 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: 6606 1.34 - 1.47: 5596 1.47 - 1.59: 9282 1.59 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 21667 Sorted by residual: bond pdb=" N ASP G 84 " pdb=" CA ASP G 84 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.23e-02 6.61e+03 1.26e+01 bond pdb=" N ASP J 167 " pdb=" CA ASP J 167 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.31e-02 5.83e+03 7.31e+00 bond pdb=" N ASP D 81 " pdb=" CA ASP D 81 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.43e+00 bond pdb=" N LEU E 125 " pdb=" CA LEU E 125 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.33e-02 5.65e+03 6.09e+00 bond pdb=" N LEU G 78 " pdb=" CA LEU G 78 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.85e+00 ... (remaining 21662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 27571 2.30 - 4.59: 1552 4.59 - 6.89: 228 6.89 - 9.18: 29 9.18 - 11.48: 6 Bond angle restraints: 29386 Sorted by residual: angle pdb=" N GLY G 85 " pdb=" CA GLY G 85 " pdb=" C GLY G 85 " ideal model delta sigma weight residual 114.40 103.40 11.00 1.11e+00 8.12e-01 9.83e+01 angle pdb=" N ASP G 84 " pdb=" CA ASP G 84 " pdb=" C ASP G 84 " ideal model delta sigma weight residual 111.33 119.03 -7.70 1.21e+00 6.83e-01 4.05e+01 angle pdb=" CB ARG L 68 " pdb=" CG ARG L 68 " pdb=" CD ARG L 68 " ideal model delta sigma weight residual 111.30 122.78 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CG LYS G 75 " pdb=" CD LYS G 75 " pdb=" CE LYS G 75 " ideal model delta sigma weight residual 111.30 122.41 -11.11 2.30e+00 1.89e-01 2.33e+01 angle pdb=" CA VAL M 12 " pdb=" CB VAL M 12 " pdb=" CG1 VAL M 12 " ideal model delta sigma weight residual 110.40 118.17 -7.77 1.70e+00 3.46e-01 2.09e+01 ... (remaining 29381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.90: 12998 20.90 - 41.81: 624 41.81 - 62.71: 161 62.71 - 83.61: 56 83.61 - 104.51: 29 Dihedral angle restraints: 13868 sinusoidal: 6405 harmonic: 7463 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 157.88 -64.88 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.05 -64.05 1 1.00e+01 1.00e-02 5.40e+01 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 47.97 45.03 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 13865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2654 0.069 - 0.138: 684 0.138 - 0.207: 143 0.207 - 0.276: 15 0.276 - 0.346: 1 Chirality restraints: 3497 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.86e+02 chirality pdb=" C1 MAN R 4 " pdb=" O3 BMA R 3 " pdb=" C2 MAN R 4 " pdb=" O5 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.40 2.24 0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.73e+00 ... (remaining 3494 not shown) Planarity restraints: 3687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.344 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG R 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.520 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.244 2.00e-02 2.50e+03 2.04e-01 5.22e+02 pdb=" C7 NAG R 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.342 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 538 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.15e+01 pdb=" C THR B 538 " -0.080 2.00e-02 2.50e+03 pdb=" O THR B 538 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL B 539 " 0.027 2.00e-02 2.50e+03 ... (remaining 3684 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 25 2.34 - 2.98: 10867 2.98 - 3.62: 29606 3.62 - 4.26: 50255 4.26 - 4.90: 82623 Nonbonded interactions: 173376 Sorted by model distance: nonbonded pdb=" O SER G 62 " pdb=" NH1 ARG G 66 " model vdw 1.702 3.120 nonbonded pdb=" OG1 THR A 303 " pdb=" OD1 ASP A 322 " model vdw 1.942 3.040 nonbonded pdb=" O ASN E 197 " pdb=" NH1 ARG A 308 " model vdw 1.997 3.120 nonbonded pdb=" OG SER C 35 " pdb=" O SER C 49 " model vdw 1.999 3.040 nonbonded pdb=" O VAL J 36 " pdb=" OG1 THR K 606 " model vdw 2.051 3.040 ... (remaining 173371 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 1 through 110) selection = chain 'G' selection = (chain 'M' and resid 1 through 110) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'T' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 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: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.260 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.007 0.072 21780 Z= 0.304 Angle : 1.228 17.182 29684 Z= 0.692 Chirality : 0.064 0.346 3497 Planarity : 0.009 0.294 3642 Dihedral : 13.913 104.514 8959 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.27 % Allowed : 7.72 % Favored : 92.02 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2549 helix: 0.91 (0.24), residues: 393 sheet: 1.35 (0.18), residues: 757 loop : 0.50 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 479 HIS 0.025 0.003 HIS L 34 PHE 0.030 0.003 PHE E 53 TYR 0.032 0.004 TYR L 87 ARG 0.022 0.001 ARG M 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 45) link_NAG-ASN : angle 2.26821 ( 135) link_ALPHA1-6 : bond 0.02258 ( 3) link_ALPHA1-6 : angle 2.58328 ( 9) link_BETA1-4 : bond 0.01809 ( 15) link_BETA1-4 : angle 3.87700 ( 45) link_ALPHA1-2 : bond 0.02868 ( 3) link_ALPHA1-2 : angle 3.86804 ( 9) link_ALPHA1-3 : bond 0.02034 ( 6) link_ALPHA1-3 : angle 2.56124 ( 18) hydrogen bonds : bond 0.15111 ( 616) hydrogen bonds : angle 7.10979 ( 1575) SS BOND : bond 0.01057 ( 41) SS BOND : angle 3.48997 ( 82) covalent geometry : bond 0.00667 (21667) covalent geometry : angle 1.19691 (29386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 516 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.9069 (t) cc_final: 0.8510 (p) REVERT: G 91 TYR cc_start: 0.9072 (m-80) cc_final: 0.8460 (m-80) REVERT: I 103 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7048 (tpp80) REVERT: E 305 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8126 (mtpt) REVERT: E 327 ARG cc_start: 0.5964 (mtt-85) cc_final: 0.5293 (mmt-90) REVERT: F 639 THR cc_start: 0.9236 (m) cc_final: 0.8953 (m) REVERT: C 23 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7346 (ttm110) REVERT: C 75 LYS cc_start: 0.8739 (mttp) cc_final: 0.8121 (tttp) REVERT: A 139 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7180 (mtt90) REVERT: B 638 TYR cc_start: 0.8888 (m-80) cc_final: 0.8458 (m-80) REVERT: N 53 GLN cc_start: 0.7909 (mp10) cc_final: 0.7454 (mp10) REVERT: N 61 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7404 (mtp-110) REVERT: K 625 ASN cc_start: 0.8705 (m-40) cc_final: 0.7932 (t0) REVERT: K 635 ILE cc_start: 0.8892 (tp) cc_final: 0.8675 (tt) REVERT: K 653 GLN cc_start: 0.8516 (tt0) cc_final: 0.8266 (tt0) outliers start: 6 outliers final: 1 residues processed: 521 average time/residue: 0.3307 time to fit residues: 261.2678 Evaluate side-chains 409 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 199 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 ASN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 195 ASN E 249 HIS E 352 HIS E 428 GLN F 607 ASN A 105 HIS A 114 GLN A 289 ASN A 302 ASN B 591 GLN B 607 ASN M 81 GLN J 103 GLN J 195 ASN J 425 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102648 restraints weight = 33657.768| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.60 r_work: 0.3126 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21780 Z= 0.180 Angle : 0.701 14.400 29684 Z= 0.359 Chirality : 0.047 0.196 3497 Planarity : 0.004 0.047 3642 Dihedral : 9.103 75.606 4265 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.17 % Allowed : 9.71 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2549 helix: 1.74 (0.27), residues: 411 sheet: 1.29 (0.18), residues: 766 loop : 0.16 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 479 HIS 0.006 0.001 HIS L 34 PHE 0.016 0.002 PHE E 176 TYR 0.020 0.002 TYR J 217 ARG 0.006 0.001 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 45) link_NAG-ASN : angle 2.16307 ( 135) link_ALPHA1-6 : bond 0.00675 ( 3) link_ALPHA1-6 : angle 1.58750 ( 9) link_BETA1-4 : bond 0.00633 ( 15) link_BETA1-4 : angle 2.39618 ( 45) link_ALPHA1-2 : bond 0.01135 ( 3) link_ALPHA1-2 : angle 2.75565 ( 9) link_ALPHA1-3 : bond 0.01096 ( 6) link_ALPHA1-3 : angle 1.54767 ( 18) hydrogen bonds : bond 0.04985 ( 616) hydrogen bonds : angle 5.32395 ( 1575) SS BOND : bond 0.00418 ( 41) SS BOND : angle 1.82866 ( 82) covalent geometry : bond 0.00410 (21667) covalent geometry : angle 0.67244 (29386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 416 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8553 (p) cc_final: 0.8234 (p) REVERT: G 68 THR cc_start: 0.8938 (t) cc_final: 0.8618 (p) REVERT: G 82 MET cc_start: 0.8417 (mtt) cc_final: 0.8119 (mtt) REVERT: G 91 TYR cc_start: 0.9139 (m-80) cc_final: 0.8519 (m-80) REVERT: I 21 ILE cc_start: 0.8660 (mt) cc_final: 0.8379 (tt) REVERT: I 45 LYS cc_start: 0.9239 (ttpp) cc_final: 0.8960 (ttpp) REVERT: I 95 GLN cc_start: 0.8541 (pm20) cc_final: 0.8005 (mm110) REVERT: D 50 ASP cc_start: 0.8444 (m-30) cc_final: 0.8238 (m-30) REVERT: L 22 PHE cc_start: 0.7657 (m-80) cc_final: 0.7159 (m-80) REVERT: L 24 ARG cc_start: 0.8061 (mpt180) cc_final: 0.7810 (mpt180) REVERT: A 139 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7143 (mtt90) REVERT: A 217 TYR cc_start: 0.8736 (m-80) cc_final: 0.8457 (m-80) REVERT: A 347 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7298 (mttt) REVERT: A 419 ARG cc_start: 0.8575 (mmt90) cc_final: 0.8309 (mmm-85) REVERT: M 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7947 (t0) REVERT: M 91 TYR cc_start: 0.8791 (m-80) cc_final: 0.8518 (m-80) REVERT: N 79 GLN cc_start: 0.7504 (mp10) cc_final: 0.6962 (tm-30) REVERT: J 440 GLN cc_start: 0.8504 (tp-100) cc_final: 0.7888 (tp-100) REVERT: K 635 ILE cc_start: 0.8945 (tp) cc_final: 0.8414 (tp) outliers start: 49 outliers final: 33 residues processed: 449 average time/residue: 0.3385 time to fit residues: 231.5162 Evaluate side-chains 415 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 381 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 330 HIS F 607 ASN A 114 GLN A 428 GLN M 3 GLN J 103 GLN J 249 HIS ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS K 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100941 restraints weight = 33534.343| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.61 r_work: 0.3100 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.004 0.061 21780 Z= 0.169 Angle : 0.632 10.813 29684 Z= 0.320 Chirality : 0.045 0.197 3497 Planarity : 0.004 0.049 3642 Dihedral : 7.980 68.695 4263 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.53 % Rotamer: Outliers : 2.48 % Allowed : 10.73 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2549 helix: 1.36 (0.26), residues: 435 sheet: 1.22 (0.18), residues: 741 loop : 0.04 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.005 0.001 HIS A 249 PHE 0.015 0.002 PHE H 78 TYR 0.031 0.002 TYR N 49 ARG 0.006 0.001 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 1.96951 ( 135) link_ALPHA1-6 : bond 0.00623 ( 3) link_ALPHA1-6 : angle 1.84479 ( 9) link_BETA1-4 : bond 0.00416 ( 15) link_BETA1-4 : angle 2.05676 ( 45) link_ALPHA1-2 : bond 0.01188 ( 3) link_ALPHA1-2 : angle 2.60784 ( 9) link_ALPHA1-3 : bond 0.01018 ( 6) link_ALPHA1-3 : angle 1.50261 ( 18) hydrogen bonds : bond 0.04284 ( 616) hydrogen bonds : angle 4.92570 ( 1575) SS BOND : bond 0.00625 ( 41) SS BOND : angle 1.77458 ( 82) covalent geometry : bond 0.00390 (21667) covalent geometry : angle 0.60495 (29386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 405 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8488 (p) cc_final: 0.8171 (p) REVERT: G 68 THR cc_start: 0.8946 (t) cc_final: 0.8601 (p) REVERT: G 91 TYR cc_start: 0.9176 (m-80) cc_final: 0.8601 (m-80) REVERT: I 21 ILE cc_start: 0.8628 (mt) cc_final: 0.8221 (tt) REVERT: I 45 LYS cc_start: 0.9274 (ttpp) cc_final: 0.8974 (ttpp) REVERT: H 36 TRP cc_start: 0.7447 (m100) cc_final: 0.7211 (m-90) REVERT: H 103 TRP cc_start: 0.7116 (m100) cc_final: 0.6847 (m100) REVERT: L 22 PHE cc_start: 0.7683 (m-80) cc_final: 0.7218 (m-80) REVERT: L 24 ARG cc_start: 0.8128 (mpt180) cc_final: 0.7919 (mpt180) REVERT: A 139 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7194 (mtt90) REVERT: A 217 TYR cc_start: 0.8741 (m-80) cc_final: 0.8199 (m-80) REVERT: M 72 ASP cc_start: 0.8235 (t0) cc_final: 0.7963 (t0) REVERT: M 81 GLN cc_start: 0.7891 (tm130) cc_final: 0.7610 (tm-30) REVERT: M 82 MET cc_start: 0.7902 (mtp) cc_final: 0.7673 (mtp) REVERT: N 45 LYS cc_start: 0.8700 (tttp) cc_final: 0.8430 (tttm) REVERT: N 79 GLN cc_start: 0.7482 (mp10) cc_final: 0.6932 (tm-30) REVERT: N 103 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7636 (mmm160) REVERT: J 111 LEU cc_start: 0.8447 (mt) cc_final: 0.8234 (mt) REVERT: J 440 GLN cc_start: 0.8534 (tp-100) cc_final: 0.7929 (tp-100) REVERT: K 635 ILE cc_start: 0.8950 (tp) cc_final: 0.8395 (tp) REVERT: K 653 GLN cc_start: 0.8767 (tt0) cc_final: 0.8496 (tt0) outliers start: 56 outliers final: 37 residues processed: 435 average time/residue: 0.3359 time to fit residues: 222.2383 Evaluate side-chains 410 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 239 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.0370 chunk 121 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN E 330 HIS D 31 ASN A 114 GLN A 249 HIS B 607 ASN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104025 restraints weight = 33597.352| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.53 r_work: 0.3147 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21780 Z= 0.173 Angle : 0.606 11.889 29684 Z= 0.306 Chirality : 0.045 0.218 3497 Planarity : 0.004 0.050 3642 Dihedral : 7.152 59.051 4263 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 12.33 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2549 helix: 1.31 (0.27), residues: 435 sheet: 1.17 (0.19), residues: 714 loop : -0.06 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS E 249 PHE 0.013 0.002 PHE E 176 TYR 0.026 0.002 TYR N 49 ARG 0.006 0.000 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 45) link_NAG-ASN : angle 1.88953 ( 135) link_ALPHA1-6 : bond 0.00750 ( 3) link_ALPHA1-6 : angle 1.84016 ( 9) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.84829 ( 45) link_ALPHA1-2 : bond 0.01161 ( 3) link_ALPHA1-2 : angle 2.50515 ( 9) link_ALPHA1-3 : bond 0.01185 ( 6) link_ALPHA1-3 : angle 1.57329 ( 18) hydrogen bonds : bond 0.04046 ( 616) hydrogen bonds : angle 4.72660 ( 1575) SS BOND : bond 0.00443 ( 41) SS BOND : angle 1.64601 ( 82) covalent geometry : bond 0.00402 (21667) covalent geometry : angle 0.58067 (29386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 396 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8472 (p) cc_final: 0.8175 (p) REVERT: G 68 THR cc_start: 0.8985 (t) cc_final: 0.8669 (p) REVERT: I 21 ILE cc_start: 0.8661 (mt) cc_final: 0.8226 (tt) REVERT: I 45 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8911 (ttpp) REVERT: I 95 GLN cc_start: 0.8578 (pm20) cc_final: 0.8079 (mm110) REVERT: E 66 HIS cc_start: 0.5573 (t-90) cc_final: 0.5150 (m90) REVERT: E 67 ASN cc_start: 0.7530 (t0) cc_final: 0.6952 (t0) REVERT: F 584 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 23 ARG cc_start: 0.8317 (ttm110) cc_final: 0.8048 (ttm110) REVERT: D 85 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: H 25 SER cc_start: 0.6516 (m) cc_final: 0.5902 (t) REVERT: H 36 TRP cc_start: 0.7379 (m100) cc_final: 0.7087 (m-90) REVERT: H 103 TRP cc_start: 0.7165 (m100) cc_final: 0.6924 (m100) REVERT: L 22 PHE cc_start: 0.7644 (m-80) cc_final: 0.7076 (m-80) REVERT: L 24 ARG cc_start: 0.8145 (mpt180) cc_final: 0.7888 (mpt180) REVERT: A 106 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7604 (mt-10) REVERT: A 139 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7164 (mtt90) REVERT: B 632 ASP cc_start: 0.9208 (t0) cc_final: 0.9000 (t0) REVERT: M 72 ASP cc_start: 0.8281 (t0) cc_final: 0.8010 (t0) REVERT: N 61 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7687 (mtm110) REVERT: J 166 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8294 (ttp-110) REVERT: J 440 GLN cc_start: 0.8442 (tp-100) cc_final: 0.7894 (tp-100) REVERT: K 607 ASN cc_start: 0.8988 (t0) cc_final: 0.8777 (t0) REVERT: K 635 ILE cc_start: 0.8979 (tp) cc_final: 0.8420 (tp) outliers start: 59 outliers final: 42 residues processed: 429 average time/residue: 0.3398 time to fit residues: 222.5729 Evaluate side-chains 417 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain J residue 430 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 607 ASN D 31 ASN A 114 GLN A 216 HIS B 607 ASN M 3 GLN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098468 restraints weight = 33680.780| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.48 r_work: 0.3062 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 21780 Z= 0.318 Angle : 0.724 12.736 29684 Z= 0.362 Chirality : 0.049 0.226 3497 Planarity : 0.005 0.053 3642 Dihedral : 7.344 59.228 4263 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 3.37 % Allowed : 13.13 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.16), residues: 2549 helix: 1.01 (0.26), residues: 429 sheet: 0.84 (0.19), residues: 720 loop : -0.33 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 479 HIS 0.006 0.001 HIS J 249 PHE 0.016 0.002 PHE E 353 TYR 0.030 0.002 TYR N 49 ARG 0.013 0.001 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 45) link_NAG-ASN : angle 2.15605 ( 135) link_ALPHA1-6 : bond 0.00773 ( 3) link_ALPHA1-6 : angle 1.85465 ( 9) link_BETA1-4 : bond 0.00342 ( 15) link_BETA1-4 : angle 1.98303 ( 45) link_ALPHA1-2 : bond 0.01122 ( 3) link_ALPHA1-2 : angle 2.40551 ( 9) link_ALPHA1-3 : bond 0.00922 ( 6) link_ALPHA1-3 : angle 1.88518 ( 18) hydrogen bonds : bond 0.04732 ( 616) hydrogen bonds : angle 4.98395 ( 1575) SS BOND : bond 0.00622 ( 41) SS BOND : angle 1.94938 ( 82) covalent geometry : bond 0.00760 (21667) covalent geometry : angle 0.69699 (29386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 379 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8504 (p) cc_final: 0.8223 (p) REVERT: G 68 THR cc_start: 0.9034 (t) cc_final: 0.8717 (p) REVERT: I 21 ILE cc_start: 0.8704 (mt) cc_final: 0.8145 (tt) REVERT: I 45 LYS cc_start: 0.9280 (ttpp) cc_final: 0.8946 (ttpp) REVERT: I 95 GLN cc_start: 0.8597 (pm20) cc_final: 0.8264 (mp10) REVERT: F 584 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8454 (mt-10) REVERT: C 23 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8147 (ttm110) REVERT: D 47 MET cc_start: 0.8380 (mmt) cc_final: 0.8068 (mmt) REVERT: D 85 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: H 25 SER cc_start: 0.6484 (m) cc_final: 0.6186 (t) REVERT: H 36 TRP cc_start: 0.7542 (m100) cc_final: 0.7172 (m-90) REVERT: H 103 TRP cc_start: 0.7321 (m100) cc_final: 0.7005 (m100) REVERT: A 78 ASP cc_start: 0.7447 (t0) cc_final: 0.7111 (t0) REVERT: A 106 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7664 (mt-10) REVERT: A 161 MET cc_start: 0.8687 (tpt) cc_final: 0.8353 (tpt) REVERT: A 217 TYR cc_start: 0.8893 (m-80) cc_final: 0.8336 (m-80) REVERT: A 308 ARG cc_start: 0.8128 (mpp80) cc_final: 0.7834 (mtt90) REVERT: B 632 ASP cc_start: 0.9243 (t0) cc_final: 0.9025 (t0) REVERT: B 638 TYR cc_start: 0.8943 (m-80) cc_final: 0.8646 (m-80) REVERT: M 72 ASP cc_start: 0.8305 (t0) cc_final: 0.8001 (t0) REVERT: J 207 LYS cc_start: 0.8180 (pttt) cc_final: 0.7848 (mmmt) REVERT: J 440 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8099 (tp-100) REVERT: K 635 ILE cc_start: 0.9075 (tp) cc_final: 0.8510 (tp) outliers start: 76 outliers final: 61 residues processed: 424 average time/residue: 0.3320 time to fit residues: 215.3470 Evaluate side-chains 428 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 366 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 346 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain K residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 207 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 164 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN E 330 HIS F 607 ASN D 31 ASN H 39 GLN L 38 GLN A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103682 restraints weight = 33463.254| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.51 r_work: 0.3140 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21780 Z= 0.123 Angle : 0.576 10.784 29684 Z= 0.290 Chirality : 0.044 0.199 3497 Planarity : 0.004 0.051 3642 Dihedral : 6.499 58.229 4263 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 2.48 % Allowed : 14.41 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2549 helix: 1.24 (0.27), residues: 435 sheet: 0.77 (0.19), residues: 734 loop : -0.23 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.004 0.001 HIS A 249 PHE 0.017 0.001 PHE E 53 TYR 0.029 0.001 TYR N 49 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 45) link_NAG-ASN : angle 1.83439 ( 135) link_ALPHA1-6 : bond 0.00984 ( 3) link_ALPHA1-6 : angle 1.36271 ( 9) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.48429 ( 45) link_ALPHA1-2 : bond 0.01130 ( 3) link_ALPHA1-2 : angle 2.44085 ( 9) link_ALPHA1-3 : bond 0.01143 ( 6) link_ALPHA1-3 : angle 1.50411 ( 18) hydrogen bonds : bond 0.03762 ( 616) hydrogen bonds : angle 4.58782 ( 1575) SS BOND : bond 0.00415 ( 41) SS BOND : angle 1.45603 ( 82) covalent geometry : bond 0.00276 (21667) covalent geometry : angle 0.55339 (29386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 407 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 TYR cc_start: 0.8779 (p90) cc_final: 0.8517 (p90) REVERT: G 68 THR cc_start: 0.8942 (t) cc_final: 0.8675 (p) REVERT: G 81 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8543 (mm110) REVERT: I 21 ILE cc_start: 0.8643 (mt) cc_final: 0.8068 (tt) REVERT: I 45 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8879 (ttpp) REVERT: I 95 GLN cc_start: 0.8537 (pm20) cc_final: 0.8254 (mm110) REVERT: E 66 HIS cc_start: 0.5550 (t-90) cc_final: 0.5153 (m90) REVERT: E 304 VAL cc_start: 0.9496 (t) cc_final: 0.9279 (p) REVERT: E 327 ARG cc_start: 0.6001 (mtt180) cc_final: 0.5270 (mmt-90) REVERT: D 49 TYR cc_start: 0.8860 (p90) cc_final: 0.8190 (p90) REVERT: D 85 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: H 25 SER cc_start: 0.6606 (m) cc_final: 0.6117 (t) REVERT: H 36 TRP cc_start: 0.7385 (m100) cc_final: 0.6882 (m100) REVERT: H 70 SER cc_start: 0.7729 (t) cc_final: 0.7387 (p) REVERT: H 103 TRP cc_start: 0.7202 (m100) cc_final: 0.6891 (m100) REVERT: L 24 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7784 (mmt-90) REVERT: L 42 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7217 (mp10) REVERT: A 78 ASP cc_start: 0.7438 (t0) cc_final: 0.7103 (t0) REVERT: A 99 ASN cc_start: 0.8896 (t0) cc_final: 0.8361 (t0) REVERT: A 106 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7678 (mt-10) REVERT: A 308 ARG cc_start: 0.8076 (mpp80) cc_final: 0.7594 (mtt90) REVERT: A 370 GLU cc_start: 0.8385 (tt0) cc_final: 0.8163 (tt0) REVERT: A 419 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8367 (mmm-85) REVERT: B 632 ASP cc_start: 0.9191 (t0) cc_final: 0.8937 (t0) REVERT: M 72 ASP cc_start: 0.8257 (t0) cc_final: 0.7971 (t0) REVERT: N 61 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7553 (ttp80) REVERT: J 440 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7885 (tp-100) REVERT: K 635 ILE cc_start: 0.8951 (tp) cc_final: 0.8380 (tp) outliers start: 56 outliers final: 35 residues processed: 433 average time/residue: 0.3417 time to fit residues: 227.4349 Evaluate side-chains 421 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 231 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS D 31 ASN H 39 GLN L 38 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 607 ASN N 37 GLN N 79 GLN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 591 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102759 restraints weight = 33797.428| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.47 r_work: 0.3087 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21780 Z= 0.237 Angle : 0.649 11.437 29684 Z= 0.325 Chirality : 0.046 0.304 3497 Planarity : 0.004 0.054 3642 Dihedral : 6.475 58.288 4263 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.66 % Allowed : 15.12 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2549 helix: 1.18 (0.27), residues: 429 sheet: 0.69 (0.19), residues: 749 loop : -0.38 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.005 0.001 HIS J 249 PHE 0.015 0.002 PHE L 71 TYR 0.027 0.002 TYR N 49 ARG 0.008 0.001 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 45) link_NAG-ASN : angle 2.05854 ( 135) link_ALPHA1-6 : bond 0.00977 ( 3) link_ALPHA1-6 : angle 1.33175 ( 9) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.67773 ( 45) link_ALPHA1-2 : bond 0.01093 ( 3) link_ALPHA1-2 : angle 2.38476 ( 9) link_ALPHA1-3 : bond 0.00963 ( 6) link_ALPHA1-3 : angle 1.74526 ( 18) hydrogen bonds : bond 0.04190 ( 616) hydrogen bonds : angle 4.73535 ( 1575) SS BOND : bond 0.00568 ( 41) SS BOND : angle 1.86405 ( 82) covalent geometry : bond 0.00568 (21667) covalent geometry : angle 0.62315 (29386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 372 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.9008 (t) cc_final: 0.8658 (p) REVERT: G 82 MET cc_start: 0.8375 (mtt) cc_final: 0.7715 (mtm) REVERT: I 21 ILE cc_start: 0.8688 (mt) cc_final: 0.8101 (tt) REVERT: I 45 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8939 (ttpp) REVERT: I 73 LEU cc_start: 0.8840 (tp) cc_final: 0.8615 (tp) REVERT: I 95 GLN cc_start: 0.8597 (pm20) cc_final: 0.8342 (mp10) REVERT: E 66 HIS cc_start: 0.5671 (t-90) cc_final: 0.5302 (m90) REVERT: F 584 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8512 (mt-10) REVERT: D 49 TYR cc_start: 0.8964 (p90) cc_final: 0.8378 (p90) REVERT: D 85 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: H 25 SER cc_start: 0.6591 (m) cc_final: 0.6344 (t) REVERT: H 103 TRP cc_start: 0.7273 (m100) cc_final: 0.6924 (m100) REVERT: L 22 PHE cc_start: 0.7608 (m-80) cc_final: 0.6973 (m-80) REVERT: L 24 ARG cc_start: 0.8214 (mmt-90) cc_final: 0.7802 (mpt180) REVERT: A 78 ASP cc_start: 0.7446 (t0) cc_final: 0.7136 (t0) REVERT: A 106 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7684 (mt-10) REVERT: A 308 ARG cc_start: 0.8109 (mpp80) cc_final: 0.7659 (mtt90) REVERT: B 632 ASP cc_start: 0.9216 (t0) cc_final: 0.8987 (t0) REVERT: M 72 ASP cc_start: 0.8251 (t0) cc_final: 0.7951 (t0) REVERT: N 61 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7524 (ttp80) REVERT: J 141 MET cc_start: 0.7948 (ttp) cc_final: 0.7748 (ttt) REVERT: J 440 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8096 (tp-100) REVERT: K 635 ILE cc_start: 0.9020 (tp) cc_final: 0.8455 (tp) outliers start: 60 outliers final: 48 residues processed: 404 average time/residue: 0.3436 time to fit residues: 211.5700 Evaluate side-chains 413 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 607 ASN D 31 ASN H 39 GLN L 38 GLN L 53 ASN A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102975 restraints weight = 33639.667| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.54 r_work: 0.3125 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21780 Z= 0.144 Angle : 0.589 11.490 29684 Z= 0.296 Chirality : 0.044 0.195 3497 Planarity : 0.004 0.053 3642 Dihedral : 6.124 56.952 4263 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 2.57 % Allowed : 15.57 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2549 helix: 1.21 (0.27), residues: 435 sheet: 0.73 (0.19), residues: 697 loop : -0.39 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS J 249 PHE 0.018 0.001 PHE L 71 TYR 0.029 0.001 TYR N 49 ARG 0.008 0.000 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 45) link_NAG-ASN : angle 2.00775 ( 135) link_ALPHA1-6 : bond 0.01004 ( 3) link_ALPHA1-6 : angle 1.24247 ( 9) link_BETA1-4 : bond 0.00339 ( 15) link_BETA1-4 : angle 1.46957 ( 45) link_ALPHA1-2 : bond 0.01111 ( 3) link_ALPHA1-2 : angle 2.41655 ( 9) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 1.49170 ( 18) hydrogen bonds : bond 0.03800 ( 616) hydrogen bonds : angle 4.59120 ( 1575) SS BOND : bond 0.00492 ( 41) SS BOND : angle 1.57957 ( 82) covalent geometry : bond 0.00338 (21667) covalent geometry : angle 0.56399 (29386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.8973 (t) cc_final: 0.8663 (p) REVERT: G 81 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8526 (mm110) REVERT: G 82 MET cc_start: 0.8415 (mtt) cc_final: 0.7741 (mtm) REVERT: I 21 ILE cc_start: 0.8642 (mt) cc_final: 0.8025 (tt) REVERT: I 45 LYS cc_start: 0.9273 (ttpp) cc_final: 0.8915 (ttpp) REVERT: I 73 LEU cc_start: 0.8835 (tp) cc_final: 0.8611 (tp) REVERT: I 95 GLN cc_start: 0.8559 (pm20) cc_final: 0.8299 (mm110) REVERT: E 66 HIS cc_start: 0.5692 (t-90) cc_final: 0.5377 (m90) REVERT: E 304 VAL cc_start: 0.9508 (t) cc_final: 0.9303 (p) REVERT: D 47 MET cc_start: 0.7994 (mmt) cc_final: 0.7571 (mmt) REVERT: D 49 TYR cc_start: 0.8911 (p90) cc_final: 0.8189 (p90) REVERT: D 85 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: H 25 SER cc_start: 0.6656 (m) cc_final: 0.6363 (t) REVERT: H 98 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7943 (tt) REVERT: H 100 ILE cc_start: 0.8687 (pt) cc_final: 0.8457 (mt) REVERT: H 103 TRP cc_start: 0.7181 (m100) cc_final: 0.6811 (m100) REVERT: L 22 PHE cc_start: 0.7691 (m-80) cc_final: 0.7039 (m-80) REVERT: L 24 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7749 (mpt180) REVERT: L 42 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7312 (mp10) REVERT: L 88 CYS cc_start: 0.5022 (p) cc_final: 0.4662 (p) REVERT: L 98 PHE cc_start: 0.7875 (m-80) cc_final: 0.7490 (m-80) REVERT: A 78 ASP cc_start: 0.7454 (t0) cc_final: 0.7179 (t0) REVERT: A 99 ASN cc_start: 0.8883 (t0) cc_final: 0.8317 (t0) REVERT: A 106 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7671 (mt-10) REVERT: A 217 TYR cc_start: 0.8762 (m-80) cc_final: 0.8047 (m-80) REVERT: A 370 GLU cc_start: 0.8412 (tt0) cc_final: 0.8164 (tt0) REVERT: A 419 ARG cc_start: 0.8665 (mmt90) cc_final: 0.8413 (mmm-85) REVERT: B 632 ASP cc_start: 0.9198 (t0) cc_final: 0.8976 (t0) REVERT: M 72 ASP cc_start: 0.8257 (t0) cc_final: 0.7953 (t0) REVERT: J 414 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7899 (tt) REVERT: J 440 GLN cc_start: 0.8419 (tp-100) cc_final: 0.7899 (tp-100) REVERT: K 635 ILE cc_start: 0.8941 (tp) cc_final: 0.8363 (tp) REVERT: K 653 GLN cc_start: 0.8806 (tt0) cc_final: 0.8573 (tt0) outliers start: 58 outliers final: 45 residues processed: 416 average time/residue: 0.3310 time to fit residues: 211.6985 Evaluate side-chains 426 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 377 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 234 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 248 optimal weight: 0.0970 chunk 189 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN F 616 ASN D 31 ASN A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101263 restraints weight = 33586.750| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.47 r_work: 0.3102 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21780 Z= 0.197 Angle : 0.621 12.180 29684 Z= 0.312 Chirality : 0.045 0.205 3497 Planarity : 0.004 0.053 3642 Dihedral : 6.155 55.112 4263 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.75 % Allowed : 15.43 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2549 helix: 1.22 (0.27), residues: 429 sheet: 0.67 (0.20), residues: 685 loop : -0.41 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.005 0.001 HIS J 249 PHE 0.017 0.002 PHE L 71 TYR 0.030 0.001 TYR N 49 ARG 0.009 0.001 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 45) link_NAG-ASN : angle 2.06639 ( 135) link_ALPHA1-6 : bond 0.00943 ( 3) link_ALPHA1-6 : angle 1.28741 ( 9) link_BETA1-4 : bond 0.00286 ( 15) link_BETA1-4 : angle 1.58602 ( 45) link_ALPHA1-2 : bond 0.01001 ( 3) link_ALPHA1-2 : angle 2.36987 ( 9) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 1.62265 ( 18) hydrogen bonds : bond 0.04034 ( 616) hydrogen bonds : angle 4.68294 ( 1575) SS BOND : bond 0.00541 ( 41) SS BOND : angle 1.69160 ( 82) covalent geometry : bond 0.00469 (21667) covalent geometry : angle 0.59535 (29386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 82 MET cc_start: 0.8375 (mtt) cc_final: 0.7670 (mtm) REVERT: I 21 ILE cc_start: 0.8679 (mt) cc_final: 0.8063 (tt) REVERT: I 45 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8932 (ttpp) REVERT: I 95 GLN cc_start: 0.8600 (pm20) cc_final: 0.8357 (mp10) REVERT: E 66 HIS cc_start: 0.5687 (t-90) cc_final: 0.5379 (m90) REVERT: D 85 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: H 36 TRP cc_start: 0.7508 (m100) cc_final: 0.7212 (m-90) REVERT: H 100 ILE cc_start: 0.8706 (pt) cc_final: 0.8499 (mt) REVERT: H 103 TRP cc_start: 0.7222 (m100) cc_final: 0.6868 (m100) REVERT: L 22 PHE cc_start: 0.7699 (m-80) cc_final: 0.7048 (m-80) REVERT: L 24 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7747 (mpt180) REVERT: L 42 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7329 (mp10) REVERT: A 78 ASP cc_start: 0.7484 (t0) cc_final: 0.7209 (t0) REVERT: A 106 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7767 (mt-10) REVERT: A 217 TYR cc_start: 0.8785 (m-80) cc_final: 0.8083 (m-80) REVERT: A 308 ARG cc_start: 0.8057 (mpp80) cc_final: 0.7651 (mtt90) REVERT: A 419 ARG cc_start: 0.8691 (mmt90) cc_final: 0.8439 (mmm-85) REVERT: M 72 ASP cc_start: 0.8240 (t0) cc_final: 0.7930 (t0) REVERT: J 153 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: J 414 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (tt) REVERT: J 440 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8084 (tp-100) REVERT: K 635 ILE cc_start: 0.9005 (tp) cc_final: 0.8436 (tp) outliers start: 62 outliers final: 50 residues processed: 404 average time/residue: 0.3360 time to fit residues: 208.0252 Evaluate side-chains 419 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 366 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 28 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101465 restraints weight = 34108.314| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.56 r_work: 0.3094 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21780 Z= 0.173 Angle : 0.611 12.326 29684 Z= 0.308 Chirality : 0.045 0.201 3497 Planarity : 0.004 0.054 3642 Dihedral : 6.051 50.277 4263 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.53 % Allowed : 16.05 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2549 helix: 1.15 (0.27), residues: 435 sheet: 0.70 (0.20), residues: 685 loop : -0.46 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.005 0.001 HIS J 249 PHE 0.019 0.002 PHE L 71 TYR 0.030 0.001 TYR N 49 ARG 0.010 0.001 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 45) link_NAG-ASN : angle 1.99043 ( 135) link_ALPHA1-6 : bond 0.00922 ( 3) link_ALPHA1-6 : angle 1.28086 ( 9) link_BETA1-4 : bond 0.00290 ( 15) link_BETA1-4 : angle 1.53472 ( 45) link_ALPHA1-2 : bond 0.01084 ( 3) link_ALPHA1-2 : angle 2.32867 ( 9) link_ALPHA1-3 : bond 0.00919 ( 6) link_ALPHA1-3 : angle 1.53149 ( 18) hydrogen bonds : bond 0.03942 ( 616) hydrogen bonds : angle 4.64896 ( 1575) SS BOND : bond 0.00517 ( 41) SS BOND : angle 1.68573 ( 82) covalent geometry : bond 0.00412 (21667) covalent geometry : angle 0.58656 (29386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 TYR cc_start: 0.8743 (p90) cc_final: 0.8493 (p90) REVERT: G 82 MET cc_start: 0.8399 (mtt) cc_final: 0.7736 (mtm) REVERT: I 21 ILE cc_start: 0.8664 (mt) cc_final: 0.8023 (tt) REVERT: I 45 LYS cc_start: 0.9291 (ttpp) cc_final: 0.8954 (ttpp) REVERT: I 95 GLN cc_start: 0.8615 (pm20) cc_final: 0.8365 (mp10) REVERT: D 49 TYR cc_start: 0.8905 (p90) cc_final: 0.8225 (p90) REVERT: D 85 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: H 36 TRP cc_start: 0.7571 (m100) cc_final: 0.7323 (m-90) REVERT: H 100 ILE cc_start: 0.8693 (pt) cc_final: 0.8469 (mt) REVERT: H 103 TRP cc_start: 0.7204 (m100) cc_final: 0.6851 (m100) REVERT: L 22 PHE cc_start: 0.7689 (m-80) cc_final: 0.7015 (m-80) REVERT: L 24 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7731 (mpt180) REVERT: L 42 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7274 (mp10) REVERT: L 88 CYS cc_start: 0.4943 (p) cc_final: 0.4625 (p) REVERT: A 78 ASP cc_start: 0.7530 (t0) cc_final: 0.7258 (t0) REVERT: A 106 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7758 (mt-10) REVERT: A 217 TYR cc_start: 0.8781 (m-80) cc_final: 0.8097 (m-80) REVERT: A 419 ARG cc_start: 0.8695 (mmt90) cc_final: 0.8446 (mmm-85) REVERT: M 72 ASP cc_start: 0.8247 (t0) cc_final: 0.7944 (t0) REVERT: J 153 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: J 414 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7937 (tt) REVERT: J 440 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8076 (tp-100) REVERT: K 635 ILE cc_start: 0.9001 (tp) cc_final: 0.8424 (tp) outliers start: 57 outliers final: 50 residues processed: 401 average time/residue: 0.3260 time to fit residues: 200.3061 Evaluate side-chains 420 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 167 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN A 114 GLN B 607 ASN B 652 GLN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100677 restraints weight = 33714.453| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.51 r_work: 0.3100 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.287 21780 Z= 0.228 Angle : 0.828 59.183 29684 Z= 0.471 Chirality : 0.057 1.961 3497 Planarity : 0.005 0.172 3642 Dihedral : 6.083 50.272 4263 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 2.62 % Allowed : 15.83 % Favored : 81.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2549 helix: 1.15 (0.27), residues: 435 sheet: 0.70 (0.20), residues: 685 loop : -0.46 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS J 249 PHE 0.016 0.002 PHE L 71 TYR 0.028 0.001 TYR N 49 ARG 0.009 0.000 ARG I 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 45) link_NAG-ASN : angle 1.99113 ( 135) link_ALPHA1-6 : bond 0.00925 ( 3) link_ALPHA1-6 : angle 1.28059 ( 9) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.52834 ( 45) link_ALPHA1-2 : bond 0.01060 ( 3) link_ALPHA1-2 : angle 2.32898 ( 9) link_ALPHA1-3 : bond 0.00933 ( 6) link_ALPHA1-3 : angle 1.53602 ( 18) hydrogen bonds : bond 0.03918 ( 616) hydrogen bonds : angle 4.64858 ( 1575) SS BOND : bond 0.01886 ( 41) SS BOND : angle 3.30741 ( 82) covalent geometry : bond 0.00505 (21667) covalent geometry : angle 0.79755 (29386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12260.83 seconds wall clock time: 213 minutes 2.18 seconds (12782.18 seconds total)