Starting phenix.real_space_refine on Thu Sep 18 23:30:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfv_43190/09_2025/8vfv_43190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfv_43190/09_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_43190/09_2025/8vfv_43190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfv_43190/09_2025/8vfv_43190.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfv_43190/09_2025/8vfv_43190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfv_43190/09_2025/8vfv_43190.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.74, per 1000 atoms: 0.22 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: 1.63 Conformation dependent library (CDL) restraints added in 759.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.70 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: 4.09 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 4.890 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.690 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 : 2.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (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 ARG 0.022 0.001 ARG M 66 TYR 0.032 0.004 TYR L 87 PHE 0.030 0.003 PHE E 53 TRP 0.030 0.003 TRP A 479 HIS 0.025 0.003 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00667 (21667) covalent geometry : angle 1.19691 (29386) SS BOND : bond 0.01057 ( 41) SS BOND : angle 3.48997 ( 82) hydrogen bonds : bond 0.15111 ( 616) hydrogen bonds : angle 7.10979 ( 1575) 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) 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_NAG-ASN : bond 0.00572 ( 45) link_NAG-ASN : angle 2.26821 ( 135) *********************** 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 : 0.657 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: 0.8509 (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: 0.7049 (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: 0.8122 (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: 0.7456 (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: 0.8267 (tt0) outliers start: 6 outliers final: 1 residues processed: 521 average time/residue: 0.1533 time to fit residues: 121.4574 Evaluate side-chains 408 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 76 ASN 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 249 HIS A 289 ASN B 591 GLN B 607 ASN M 81 GLN N 37 GLN J 103 GLN 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 = 0.3695 r_free = 0.3695 target = 0.135107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105490 restraints weight = 33502.409| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.61 r_work: 0.3169 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21780 Z= 0.144 Angle : 0.682 14.639 29684 Z= 0.348 Chirality : 0.047 0.203 3497 Planarity : 0.004 0.045 3642 Dihedral : 9.025 75.091 4265 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.04 % Allowed : 9.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.16), residues: 2549 helix: 1.77 (0.27), residues: 411 sheet: 1.33 (0.18), residues: 773 loop : 0.17 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.020 0.002 TYR G 100F PHE 0.016 0.002 PHE L 62 TRP 0.021 0.001 TRP E 479 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00314 (21667) covalent geometry : angle 0.65335 (29386) SS BOND : bond 0.00472 ( 41) SS BOND : angle 1.81161 ( 82) hydrogen bonds : bond 0.04762 ( 616) hydrogen bonds : angle 5.28440 ( 1575) link_ALPHA1-2 : bond 0.01144 ( 3) link_ALPHA1-2 : angle 2.78341 ( 9) link_ALPHA1-3 : bond 0.01139 ( 6) link_ALPHA1-3 : angle 1.49312 ( 18) link_ALPHA1-6 : bond 0.00722 ( 3) link_ALPHA1-6 : angle 1.57295 ( 9) link_BETA1-4 : bond 0.00645 ( 15) link_BETA1-4 : angle 2.30086 ( 45) link_NAG-ASN : bond 0.00396 ( 45) link_NAG-ASN : angle 2.13124 ( 135) *********************** 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 473 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8537 (p) cc_final: 0.8213 (p) REVERT: G 68 THR cc_start: 0.8897 (t) cc_final: 0.8607 (p) REVERT: G 82 MET cc_start: 0.8364 (mtt) cc_final: 0.8088 (mtt) REVERT: G 91 TYR cc_start: 0.9104 (m-80) cc_final: 0.8543 (m-80) REVERT: I 21 ILE cc_start: 0.8647 (mt) cc_final: 0.8389 (tt) REVERT: I 45 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8935 (ttpp) REVERT: E 360 ARG cc_start: 0.7381 (ttm170) cc_final: 0.7147 (ttt-90) REVERT: C 91 TYR cc_start: 0.8397 (m-80) cc_final: 0.7600 (m-80) REVERT: H 36 TRP cc_start: 0.7186 (m100) cc_final: 0.6792 (m100) REVERT: L 22 PHE cc_start: 0.7709 (m-80) cc_final: 0.7239 (m-80) REVERT: A 139 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7107 (mtt90) REVERT: A 217 TYR cc_start: 0.8688 (m-80) cc_final: 0.8400 (m-80) REVERT: A 347 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7258 (mttt) REVERT: N 79 GLN cc_start: 0.7328 (mp10) cc_final: 0.6908 (tm-30) REVERT: J 440 GLN cc_start: 0.8487 (tp-100) cc_final: 0.7885 (tp-100) REVERT: K 625 ASN cc_start: 0.8669 (m-40) cc_final: 0.8200 (t0) REVERT: K 635 ILE cc_start: 0.8901 (tp) cc_final: 0.8522 (tt) REVERT: K 653 GLN cc_start: 0.8676 (tt0) cc_final: 0.8434 (tt0) outliers start: 46 outliers final: 29 residues processed: 456 average time/residue: 0.1598 time to fit residues: 111.1655 Evaluate side-chains 420 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR 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 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 F residue 544 LEU Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR 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 N residue 27 ILE 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 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain K residue 528 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 95 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 167 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 A 114 GLN M 3 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN J 249 HIS ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104836 restraints weight = 33616.685| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.62 r_work: 0.3160 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21780 Z= 0.132 Angle : 0.601 10.600 29684 Z= 0.305 Chirality : 0.044 0.190 3497 Planarity : 0.004 0.046 3642 Dihedral : 7.830 67.481 4263 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 2.39 % Allowed : 10.42 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.16), residues: 2549 helix: 1.73 (0.27), residues: 417 sheet: 1.22 (0.18), residues: 771 loop : 0.10 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 50 TYR 0.029 0.001 TYR N 49 PHE 0.012 0.002 PHE E 176 TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS J 249 Details of bonding type rmsd covalent geometry : bond 0.00293 (21667) covalent geometry : angle 0.57415 (29386) SS BOND : bond 0.00503 ( 41) SS BOND : angle 1.72210 ( 82) hydrogen bonds : bond 0.04032 ( 616) hydrogen bonds : angle 4.83661 ( 1575) link_ALPHA1-2 : bond 0.01272 ( 3) link_ALPHA1-2 : angle 2.68876 ( 9) link_ALPHA1-3 : bond 0.01068 ( 6) link_ALPHA1-3 : angle 1.43434 ( 18) link_ALPHA1-6 : bond 0.00629 ( 3) link_ALPHA1-6 : angle 1.79653 ( 9) link_BETA1-4 : bond 0.00445 ( 15) link_BETA1-4 : angle 1.97570 ( 45) link_NAG-ASN : bond 0.00297 ( 45) link_NAG-ASN : angle 1.87017 ( 135) *********************** 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 475 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8491 (p) cc_final: 0.8161 (p) REVERT: G 68 THR cc_start: 0.8931 (t) cc_final: 0.8550 (p) REVERT: G 91 TYR cc_start: 0.9136 (m-80) cc_final: 0.8568 (m-80) REVERT: I 21 ILE cc_start: 0.8633 (mt) cc_final: 0.8310 (tt) REVERT: I 45 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8927 (ttpp) REVERT: E 66 HIS cc_start: 0.5236 (t-90) cc_final: 0.4870 (m90) REVERT: E 360 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7179 (ttt-90) REVERT: F 530 MET cc_start: 0.9233 (mtm) cc_final: 0.9008 (mtp) REVERT: C 100 TYR cc_start: 0.9047 (m-80) cc_final: 0.8760 (m-10) REVERT: H 36 TRP cc_start: 0.7183 (m100) cc_final: 0.6935 (m-90) REVERT: A 139 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7227 (mtt90) REVERT: M 72 ASP cc_start: 0.8256 (t0) cc_final: 0.8054 (t0) REVERT: M 81 GLN cc_start: 0.7859 (tm130) cc_final: 0.7581 (tm-30) REVERT: M 82 MET cc_start: 0.7890 (mtp) cc_final: 0.7645 (mtp) REVERT: N 31 ASN cc_start: 0.7812 (t0) cc_final: 0.7602 (t0) REVERT: J 440 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7880 (tp-100) REVERT: K 625 ASN cc_start: 0.8719 (m-40) cc_final: 0.8213 (t0) REVERT: K 635 ILE cc_start: 0.8905 (tp) cc_final: 0.8468 (tt) REVERT: K 653 GLN cc_start: 0.8676 (tt0) cc_final: 0.8461 (tt0) outliers start: 54 outliers final: 37 residues processed: 453 average time/residue: 0.1685 time to fit residues: 116.0889 Evaluate side-chains 422 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 385 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 F residue 546 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 51 VAL 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 27 ILE 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 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 430 ILE Chi-restraints excluded: chain J residue 467 THR 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 6 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 F 607 ASN D 31 ASN A 114 GLN A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3648 r_free = 0.3648 target = 0.130911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101532 restraints weight = 33584.215| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.54 r_work: 0.3102 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21780 Z= 0.257 Angle : 0.696 12.789 29684 Z= 0.350 Chirality : 0.048 0.235 3497 Planarity : 0.004 0.052 3642 Dihedral : 7.416 59.266 4263 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 3.15 % Allowed : 11.66 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2549 helix: 1.26 (0.26), residues: 429 sheet: 1.12 (0.19), residues: 714 loop : -0.12 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 103 TYR 0.028 0.002 TYR N 49 PHE 0.017 0.002 PHE E 176 TRP 0.017 0.002 TRP E 479 HIS 0.005 0.001 HIS J 249 Details of bonding type rmsd covalent geometry : bond 0.00611 (21667) covalent geometry : angle 0.66896 (29386) SS BOND : bond 0.00583 ( 41) SS BOND : angle 2.03931 ( 82) hydrogen bonds : bond 0.04576 ( 616) hydrogen bonds : angle 4.90314 ( 1575) link_ALPHA1-2 : bond 0.01122 ( 3) link_ALPHA1-2 : angle 2.47329 ( 9) link_ALPHA1-3 : bond 0.00992 ( 6) link_ALPHA1-3 : angle 1.75544 ( 18) link_ALPHA1-6 : bond 0.00731 ( 3) link_ALPHA1-6 : angle 1.93842 ( 9) link_BETA1-4 : bond 0.00356 ( 15) link_BETA1-4 : angle 2.05191 ( 45) link_NAG-ASN : bond 0.00418 ( 45) link_NAG-ASN : angle 2.05028 ( 135) *********************** 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 458 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8505 (p) cc_final: 0.8204 (p) REVERT: G 68 THR cc_start: 0.9023 (t) cc_final: 0.8660 (p) REVERT: G 81 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8553 (mm110) REVERT: I 21 ILE cc_start: 0.8697 (mt) cc_final: 0.8221 (tt) REVERT: I 45 LYS cc_start: 0.9245 (ttpp) cc_final: 0.8926 (ttpp) REVERT: I 95 GLN cc_start: 0.8605 (pm20) cc_final: 0.8188 (mm110) REVERT: E 66 HIS cc_start: 0.5663 (t-90) cc_final: 0.5257 (m90) REVERT: E 67 ASN cc_start: 0.7798 (t0) cc_final: 0.7199 (t0) REVERT: C 23 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8073 (ttm110) REVERT: D 47 MET cc_start: 0.8143 (mmt) cc_final: 0.7652 (mmt) REVERT: D 85 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: H 25 SER cc_start: 0.6521 (m) cc_final: 0.5912 (t) REVERT: H 36 TRP cc_start: 0.7375 (m100) cc_final: 0.6995 (m-90) REVERT: H 103 TRP cc_start: 0.7297 (m100) cc_final: 0.7004 (m100) REVERT: L 24 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7842 (mmt-90) REVERT: A 217 TYR cc_start: 0.8746 (m-80) cc_final: 0.8222 (m-80) REVERT: B 638 TYR cc_start: 0.8888 (m-80) cc_final: 0.8574 (m-80) REVERT: M 72 ASP cc_start: 0.8276 (t0) cc_final: 0.7998 (t0) REVERT: N 31 ASN cc_start: 0.8224 (t0) cc_final: 0.7903 (t0) REVERT: N 79 GLN cc_start: 0.7579 (mp10) cc_final: 0.6713 (tm-30) REVERT: J 116 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8581 (mp) REVERT: J 440 GLN cc_start: 0.8518 (tp-100) cc_final: 0.7949 (tp-100) REVERT: K 607 ASN cc_start: 0.9042 (t0) cc_final: 0.8800 (t0) REVERT: K 635 ILE cc_start: 0.9035 (tp) cc_final: 0.8472 (tp) outliers start: 71 outliers final: 48 residues processed: 422 average time/residue: 0.1576 time to fit residues: 101.6551 Evaluate side-chains 417 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 THR 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 104 LEU 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 195 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 607 ASN 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 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 L residue 83 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 426 MET 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 52 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 102 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 346 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 156 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 236 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 254 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN I 53 GLN E 330 HIS D 31 ASN H 39 GLN L 38 GLN A 114 GLN A 302 ASN B 607 ASN M 3 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106389 restraints weight = 33654.386| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.51 r_work: 0.3175 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21780 Z= 0.122 Angle : 0.579 11.091 29684 Z= 0.291 Chirality : 0.044 0.205 3497 Planarity : 0.004 0.052 3642 Dihedral : 6.769 57.692 4263 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 2.57 % Allowed : 13.48 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2549 helix: 1.37 (0.27), residues: 435 sheet: 1.14 (0.19), residues: 711 loop : -0.15 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 327 TYR 0.026 0.001 TYR N 49 PHE 0.010 0.001 PHE E 382 TRP 0.017 0.001 TRP E 479 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00275 (21667) covalent geometry : angle 0.55445 (29386) SS BOND : bond 0.00419 ( 41) SS BOND : angle 1.65141 ( 82) hydrogen bonds : bond 0.03786 ( 616) hydrogen bonds : angle 4.55816 ( 1575) link_ALPHA1-2 : bond 0.01117 ( 3) link_ALPHA1-2 : angle 2.52374 ( 9) link_ALPHA1-3 : bond 0.01150 ( 6) link_ALPHA1-3 : angle 1.50924 ( 18) link_ALPHA1-6 : bond 0.00848 ( 3) link_ALPHA1-6 : angle 1.64066 ( 9) link_BETA1-4 : bond 0.00390 ( 15) link_BETA1-4 : angle 1.58796 ( 45) link_NAG-ASN : bond 0.00286 ( 45) link_NAG-ASN : angle 1.81986 ( 135) *********************** 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 453 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 395 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8491 (p) cc_final: 0.8200 (p) REVERT: G 68 THR cc_start: 0.8935 (t) cc_final: 0.8642 (p) REVERT: G 81 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8562 (mm110) REVERT: I 21 ILE cc_start: 0.8683 (mt) cc_final: 0.8208 (tt) REVERT: I 45 LYS cc_start: 0.9225 (ttpp) cc_final: 0.8947 (ttpp) REVERT: I 95 GLN cc_start: 0.8557 (pm20) cc_final: 0.8153 (mm110) REVERT: E 66 HIS cc_start: 0.5601 (t-90) cc_final: 0.5253 (m90) REVERT: E 67 ASN cc_start: 0.7585 (t0) cc_final: 0.7038 (t0) REVERT: E 360 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7550 (ttt-90) REVERT: C 23 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8099 (ttm110) REVERT: D 47 MET cc_start: 0.7977 (mmt) cc_final: 0.7620 (mmt) REVERT: D 49 TYR cc_start: 0.8863 (p90) cc_final: 0.8525 (p90) REVERT: D 85 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: H 25 SER cc_start: 0.6427 (m) cc_final: 0.6099 (t) REVERT: H 36 TRP cc_start: 0.7355 (m100) cc_final: 0.6911 (m100) REVERT: H 103 TRP cc_start: 0.7180 (m100) cc_final: 0.6927 (m100) REVERT: A 106 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7652 (mt-10) REVERT: M 72 ASP cc_start: 0.8252 (t0) cc_final: 0.7976 (t0) REVERT: N 31 ASN cc_start: 0.8174 (t0) cc_final: 0.7718 (t0) REVERT: N 79 GLN cc_start: 0.7631 (mp10) cc_final: 0.7066 (tm-30) REVERT: J 166 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8282 (ttp-110) REVERT: J 440 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7838 (tp-100) REVERT: K 591 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8953 (tt0) REVERT: K 635 ILE cc_start: 0.8947 (tp) cc_final: 0.8374 (tp) outliers start: 58 outliers final: 39 residues processed: 423 average time/residue: 0.1605 time to fit residues: 103.6964 Evaluate side-chains 417 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 5 THR 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 104 LEU 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 F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER 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 L residue 58 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 247 CYS 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 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 430 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 D 31 ASN H 39 GLN L 38 GLN A 114 GLN B 607 ASN M 3 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105021 restraints weight = 33461.316| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.53 r_work: 0.3160 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21780 Z= 0.134 Angle : 0.572 10.375 29684 Z= 0.288 Chirality : 0.044 0.320 3497 Planarity : 0.004 0.050 3642 Dihedral : 6.188 58.848 4263 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 2.62 % Allowed : 13.84 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2549 helix: 1.38 (0.27), residues: 435 sheet: 1.17 (0.19), residues: 713 loop : -0.19 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.030 0.001 TYR N 49 PHE 0.019 0.002 PHE L 71 TRP 0.015 0.001 TRP E 479 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00312 (21667) covalent geometry : angle 0.54872 (29386) SS BOND : bond 0.00513 ( 41) SS BOND : angle 1.61237 ( 82) hydrogen bonds : bond 0.03678 ( 616) hydrogen bonds : angle 4.46348 ( 1575) link_ALPHA1-2 : bond 0.01073 ( 3) link_ALPHA1-2 : angle 2.50711 ( 9) link_ALPHA1-3 : bond 0.01088 ( 6) link_ALPHA1-3 : angle 1.58498 ( 18) link_ALPHA1-6 : bond 0.00992 ( 3) link_ALPHA1-6 : angle 1.34184 ( 9) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 1.53989 ( 45) link_NAG-ASN : bond 0.00272 ( 45) link_NAG-ASN : angle 1.77289 ( 135) *********************** 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: 59 poor density : 404 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 TYR cc_start: 0.8810 (p90) cc_final: 0.8484 (p90) REVERT: G 68 THR cc_start: 0.8967 (t) cc_final: 0.8624 (p) REVERT: G 81 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8542 (mm110) REVERT: G 82 MET cc_start: 0.8297 (mtt) cc_final: 0.7590 (mtm) REVERT: I 21 ILE cc_start: 0.8695 (mt) cc_final: 0.8205 (tt) REVERT: I 45 LYS cc_start: 0.9282 (ttpp) cc_final: 0.9037 (ttpp) REVERT: I 95 GLN cc_start: 0.8533 (pm20) cc_final: 0.8213 (mm110) REVERT: E 66 HIS cc_start: 0.5596 (t-90) cc_final: 0.5257 (m90) REVERT: E 67 ASN cc_start: 0.7601 (t0) cc_final: 0.7070 (t0) REVERT: D 47 MET cc_start: 0.7820 (mmt) cc_final: 0.7521 (mmt) REVERT: D 49 TYR cc_start: 0.8856 (p90) cc_final: 0.8404 (p90) REVERT: D 85 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: H 25 SER cc_start: 0.6622 (m) cc_final: 0.6069 (t) REVERT: H 36 TRP cc_start: 0.7442 (m100) cc_final: 0.7090 (m-90) REVERT: H 103 TRP cc_start: 0.7149 (m100) cc_final: 0.6883 (m100) REVERT: L 33 MET cc_start: 0.8094 (tpp) cc_final: 0.7808 (tpp) REVERT: A 78 ASP cc_start: 0.7464 (t0) cc_final: 0.7202 (t0) REVERT: A 106 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7662 (mt-10) REVERT: A 217 TYR cc_start: 0.8614 (m-80) cc_final: 0.7965 (m-80) REVERT: M 72 ASP cc_start: 0.8243 (t0) cc_final: 0.7982 (t0) REVERT: N 31 ASN cc_start: 0.8272 (t0) cc_final: 0.7770 (t0) REVERT: N 79 GLN cc_start: 0.7676 (mp10) cc_final: 0.7010 (tm-30) REVERT: J 166 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8292 (ttp-110) REVERT: J 440 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7906 (tp-100) REVERT: K 635 ILE cc_start: 0.8938 (tp) cc_final: 0.8372 (tp) outliers start: 59 outliers final: 47 residues processed: 431 average time/residue: 0.1607 time to fit residues: 105.9186 Evaluate side-chains 436 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 387 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 26 THR 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 104 LEU 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 E residue 195 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER 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 125 LEU Chi-restraints excluded: chain A residue 247 CYS 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 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 430 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 242 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN I 53 GLN E 330 HIS ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN H 39 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.133590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104306 restraints weight = 33886.413| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.52 r_work: 0.3129 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21780 Z= 0.156 Angle : 0.595 13.239 29684 Z= 0.300 Chirality : 0.044 0.275 3497 Planarity : 0.004 0.051 3642 Dihedral : 5.941 52.036 4263 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.79 % Allowed : 14.01 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.16), residues: 2549 helix: 1.36 (0.27), residues: 435 sheet: 1.07 (0.19), residues: 713 loop : -0.21 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 103 TYR 0.028 0.001 TYR N 49 PHE 0.019 0.002 PHE L 71 TRP 0.015 0.001 TRP E 479 HIS 0.005 0.001 HIS J 249 Details of bonding type rmsd covalent geometry : bond 0.00368 (21667) covalent geometry : angle 0.56952 (29386) SS BOND : bond 0.00515 ( 41) SS BOND : angle 2.01653 ( 82) hydrogen bonds : bond 0.03755 ( 616) hydrogen bonds : angle 4.48446 ( 1575) link_ALPHA1-2 : bond 0.00991 ( 3) link_ALPHA1-2 : angle 2.47205 ( 9) link_ALPHA1-3 : bond 0.01050 ( 6) link_ALPHA1-3 : angle 1.62915 ( 18) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.22464 ( 9) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 1.52459 ( 45) link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 1.79765 ( 135) *********************** 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 456 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 393 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.8972 (t) cc_final: 0.8616 (p) REVERT: G 81 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8511 (mm110) REVERT: G 82 MET cc_start: 0.8385 (mtt) cc_final: 0.7695 (mtm) REVERT: I 21 ILE cc_start: 0.8656 (mt) cc_final: 0.8106 (tt) REVERT: I 45 LYS cc_start: 0.9268 (ttpp) cc_final: 0.9018 (ttpp) REVERT: I 95 GLN cc_start: 0.8560 (pm20) cc_final: 0.8243 (mm110) REVERT: E 66 HIS cc_start: 0.5683 (t-90) cc_final: 0.5344 (m90) REVERT: E 67 ASN cc_start: 0.7689 (t0) cc_final: 0.7126 (t0) REVERT: D 47 MET cc_start: 0.7621 (mmt) cc_final: 0.7367 (mmt) REVERT: D 49 TYR cc_start: 0.8856 (p90) cc_final: 0.8391 (p90) REVERT: D 85 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: H 25 SER cc_start: 0.6468 (m) cc_final: 0.6209 (t) REVERT: H 36 TRP cc_start: 0.7380 (m100) cc_final: 0.7116 (m100) REVERT: H 70 SER cc_start: 0.7934 (t) cc_final: 0.7444 (p) REVERT: H 103 TRP cc_start: 0.7142 (m100) cc_final: 0.6863 (m100) REVERT: L 24 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7737 (mpt180) REVERT: L 42 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7107 (mp10) REVERT: A 78 ASP cc_start: 0.7523 (t0) cc_final: 0.7250 (t0) REVERT: A 106 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7648 (mt-10) REVERT: A 161 MET cc_start: 0.8555 (tpt) cc_final: 0.8274 (tpt) REVERT: A 217 TYR cc_start: 0.8616 (m-80) cc_final: 0.7957 (m-80) REVERT: A 308 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7814 (mtt90) REVERT: A 419 ARG cc_start: 0.8676 (mmt90) cc_final: 0.8354 (mmm-85) REVERT: M 72 ASP cc_start: 0.8213 (t0) cc_final: 0.7947 (t0) REVERT: N 31 ASN cc_start: 0.8313 (t0) cc_final: 0.7787 (t0) REVERT: N 79 GLN cc_start: 0.7668 (mp10) cc_final: 0.6932 (tm-30) REVERT: J 150 MET cc_start: 0.8398 (mmm) cc_final: 0.8192 (tpp) REVERT: J 166 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8342 (ttp-110) REVERT: J 414 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7861 (tt) REVERT: J 440 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7905 (tp-100) REVERT: K 607 ASN cc_start: 0.9061 (t0) cc_final: 0.8859 (t0) REVERT: K 635 ILE cc_start: 0.8951 (tp) cc_final: 0.8370 (tp) outliers start: 63 outliers final: 47 residues processed: 423 average time/residue: 0.1739 time to fit residues: 111.8039 Evaluate side-chains 433 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 383 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 26 THR 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 104 LEU 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 E residue 195 ASN 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 546 SER 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 L residue 58 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 125 LEU 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 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 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 414 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 528 SER Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN I 53 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 607 ASN F 616 ASN D 31 ASN H 39 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099867 restraints weight = 33609.316| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.49 r_work: 0.3099 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21780 Z= 0.223 Angle : 0.651 11.544 29684 Z= 0.327 Chirality : 0.046 0.245 3497 Planarity : 0.004 0.053 3642 Dihedral : 6.142 48.209 4263 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 3.02 % Allowed : 14.32 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.16), residues: 2549 helix: 1.27 (0.27), residues: 429 sheet: 0.85 (0.19), residues: 719 loop : -0.31 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 103 TYR 0.031 0.001 TYR N 49 PHE 0.019 0.002 PHE H 78 TRP 0.015 0.001 TRP E 479 HIS 0.006 0.001 HIS J 249 Details of bonding type rmsd covalent geometry : bond 0.00534 (21667) covalent geometry : angle 0.62212 (29386) SS BOND : bond 0.00588 ( 41) SS BOND : angle 2.31381 ( 82) hydrogen bonds : bond 0.04148 ( 616) hydrogen bonds : angle 4.64699 ( 1575) link_ALPHA1-2 : bond 0.01072 ( 3) link_ALPHA1-2 : angle 2.44468 ( 9) link_ALPHA1-3 : bond 0.00903 ( 6) link_ALPHA1-3 : angle 1.70996 ( 18) link_ALPHA1-6 : bond 0.00974 ( 3) link_ALPHA1-6 : angle 1.30476 ( 9) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.65787 ( 45) link_NAG-ASN : bond 0.00366 ( 45) link_NAG-ASN : angle 1.94884 ( 135) *********************** 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 451 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 383 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.9005 (t) cc_final: 0.8652 (p) REVERT: G 82 MET cc_start: 0.8482 (mtt) cc_final: 0.7841 (mtm) REVERT: I 21 ILE cc_start: 0.8686 (mt) cc_final: 0.8079 (tt) REVERT: I 45 LYS cc_start: 0.9299 (ttpp) cc_final: 0.8953 (ttpp) REVERT: I 95 GLN cc_start: 0.8594 (pm20) cc_final: 0.8348 (mp10) REVERT: E 66 HIS cc_start: 0.5677 (t-90) cc_final: 0.5371 (m90) REVERT: E 67 ASN cc_start: 0.7854 (t0) cc_final: 0.7285 (t0) REVERT: D 47 MET cc_start: 0.7866 (mmt) cc_final: 0.7545 (mmt) REVERT: D 49 TYR cc_start: 0.8973 (p90) cc_final: 0.8393 (p90) REVERT: D 85 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: H 25 SER cc_start: 0.6562 (m) cc_final: 0.6252 (t) REVERT: H 36 TRP cc_start: 0.7466 (m100) cc_final: 0.7196 (m100) REVERT: H 103 TRP cc_start: 0.7220 (m100) cc_final: 0.6891 (m100) REVERT: L 24 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.7735 (mpt180) REVERT: L 42 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7113 (mm-40) REVERT: A 78 ASP cc_start: 0.7510 (t0) cc_final: 0.7262 (t0) REVERT: A 106 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7708 (mt-10) REVERT: A 161 MET cc_start: 0.8668 (tpt) cc_final: 0.8363 (tpt) REVERT: A 217 TYR cc_start: 0.8658 (m-80) cc_final: 0.8019 (m-80) REVERT: M 72 ASP cc_start: 0.8219 (t0) cc_final: 0.7944 (t0) REVERT: N 31 ASN cc_start: 0.8377 (t0) cc_final: 0.7831 (t0) REVERT: J 116 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8505 (mp) REVERT: J 166 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8386 (ttp-110) REVERT: J 440 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7932 (tp-100) REVERT: K 607 ASN cc_start: 0.9103 (t0) cc_final: 0.8846 (t0) REVERT: K 635 ILE cc_start: 0.9005 (tp) cc_final: 0.8424 (tp) outliers start: 68 outliers final: 54 residues processed: 412 average time/residue: 0.1729 time to fit residues: 108.6284 Evaluate side-chains 428 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 26 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 104 LEU 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 195 ASN 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 546 SER Chi-restraints excluded: chain F residue 607 ASN 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 L residue 58 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 426 MET 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 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 74 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 116 LEU Chi-restraints excluded: chain J residue 128 THR 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 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 188 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 222 optimal weight: 0.4980 chunk 198 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN H 39 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3656 r_free = 0.3656 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102588 restraints weight = 33586.058| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.52 r_work: 0.3129 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21780 Z= 0.130 Angle : 0.608 18.452 29684 Z= 0.303 Chirality : 0.044 0.193 3497 Planarity : 0.004 0.053 3642 Dihedral : 5.935 50.097 4263 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 15.17 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.16), residues: 2549 helix: 1.30 (0.27), residues: 435 sheet: 0.79 (0.19), residues: 692 loop : -0.29 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 103 TYR 0.030 0.001 TYR N 49 PHE 0.020 0.001 PHE L 71 TRP 0.018 0.001 TRP E 479 HIS 0.004 0.001 HIS J 249 Details of bonding type rmsd covalent geometry : bond 0.00302 (21667) covalent geometry : angle 0.56867 (29386) SS BOND : bond 0.00568 ( 41) SS BOND : angle 1.72038 ( 82) hydrogen bonds : bond 0.03740 ( 616) hydrogen bonds : angle 4.51961 ( 1575) link_ALPHA1-2 : bond 0.01060 ( 3) link_ALPHA1-2 : angle 2.42265 ( 9) link_ALPHA1-3 : bond 0.00982 ( 6) link_ALPHA1-3 : angle 1.49042 ( 18) link_ALPHA1-6 : bond 0.00985 ( 3) link_ALPHA1-6 : angle 1.24594 ( 9) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 1.44173 ( 45) link_NAG-ASN : bond 0.00302 ( 45) link_NAG-ASN : angle 2.75881 ( 135) *********************** 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 450 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 392 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.8968 (t) cc_final: 0.8650 (p) REVERT: G 81 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8534 (mm110) REVERT: G 82 MET cc_start: 0.8419 (mtt) cc_final: 0.7766 (mtm) REVERT: I 21 ILE cc_start: 0.8490 (mt) cc_final: 0.7900 (tt) REVERT: I 45 LYS cc_start: 0.9281 (ttpp) cc_final: 0.8932 (ttpp) REVERT: I 95 GLN cc_start: 0.8568 (pm20) cc_final: 0.8288 (mm110) REVERT: E 66 HIS cc_start: 0.5663 (t-90) cc_final: 0.5346 (m90) REVERT: E 67 ASN cc_start: 0.7706 (t0) cc_final: 0.7181 (t0) REVERT: D 47 MET cc_start: 0.7581 (mmt) cc_final: 0.7332 (mmt) REVERT: D 49 TYR cc_start: 0.8904 (p90) cc_final: 0.8241 (p90) REVERT: D 85 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: H 36 TRP cc_start: 0.7470 (m100) cc_final: 0.7240 (m100) REVERT: H 103 TRP cc_start: 0.7124 (m100) cc_final: 0.6792 (m100) REVERT: L 22 PHE cc_start: 0.7668 (m-80) cc_final: 0.7330 (m-80) REVERT: L 33 MET cc_start: 0.8090 (tpp) cc_final: 0.7816 (tpp) REVERT: L 42 GLN cc_start: 0.7338 (mm-40) cc_final: 0.7062 (mm-40) REVERT: A 78 ASP cc_start: 0.7510 (t0) cc_final: 0.7254 (t0) REVERT: A 106 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7667 (mt-10) REVERT: A 161 MET cc_start: 0.8617 (tpt) cc_final: 0.8389 (tpt) REVERT: A 217 TYR cc_start: 0.8602 (m-80) cc_final: 0.7958 (m-80) REVERT: A 419 ARG cc_start: 0.8630 (mmt90) cc_final: 0.8360 (mmm-85) REVERT: M 72 ASP cc_start: 0.8203 (t0) cc_final: 0.7955 (t0) REVERT: N 31 ASN cc_start: 0.8342 (t0) cc_final: 0.7787 (t0) REVERT: N 79 GLN cc_start: 0.7655 (mp10) cc_final: 0.6857 (tm-30) REVERT: J 166 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8357 (ttp-110) REVERT: J 440 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7891 (tp-100) REVERT: K 591 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8956 (tt0) REVERT: K 607 ASN cc_start: 0.9092 (t0) cc_final: 0.8844 (t0) REVERT: K 635 ILE cc_start: 0.8944 (tp) cc_final: 0.8355 (tp) outliers start: 58 outliers final: 44 residues processed: 420 average time/residue: 0.1699 time to fit residues: 109.1248 Evaluate side-chains 428 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 26 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 104 LEU 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 195 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER 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 58 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 247 CYS 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 62 SER 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 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 158 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 114 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 149 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN L 90 GLN A 114 GLN B 607 ASN ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104043 restraints weight = 33827.181| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.55 r_work: 0.3150 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21780 Z= 0.121 Angle : 0.579 14.608 29684 Z= 0.291 Chirality : 0.043 0.197 3497 Planarity : 0.004 0.052 3642 Dihedral : 5.657 51.503 4263 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.26 % Allowed : 15.48 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2549 helix: 1.37 (0.27), residues: 435 sheet: 0.87 (0.20), residues: 670 loop : -0.27 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 103 TYR 0.032 0.001 TYR N 49 PHE 0.018 0.001 PHE L 71 TRP 0.018 0.001 TRP E 112 HIS 0.006 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00281 (21667) covalent geometry : angle 0.54751 (29386) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.54996 ( 82) hydrogen bonds : bond 0.03536 ( 616) hydrogen bonds : angle 4.43475 ( 1575) link_ALPHA1-2 : bond 0.01088 ( 3) link_ALPHA1-2 : angle 2.34277 ( 9) link_ALPHA1-3 : bond 0.00927 ( 6) link_ALPHA1-3 : angle 1.43526 ( 18) link_ALPHA1-6 : bond 0.00913 ( 3) link_ALPHA1-6 : angle 1.25623 ( 9) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.41036 ( 45) link_NAG-ASN : bond 0.00255 ( 45) link_NAG-ASN : angle 2.38458 ( 135) ********************** 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 453 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 402 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 MET cc_start: 0.8315 (mtt) cc_final: 0.7667 (mtm) REVERT: I 21 ILE cc_start: 0.8501 (mt) cc_final: 0.7919 (tt) REVERT: I 45 LYS cc_start: 0.9274 (ttpp) cc_final: 0.8931 (ttpp) REVERT: I 95 GLN cc_start: 0.8545 (pm20) cc_final: 0.8286 (mm110) REVERT: E 66 HIS cc_start: 0.5684 (t-90) cc_final: 0.5429 (m90) REVERT: E 67 ASN cc_start: 0.7655 (t0) cc_final: 0.7160 (t0) REVERT: E 99 ASN cc_start: 0.8816 (t0) cc_final: 0.8274 (t0) REVERT: E 327 ARG cc_start: 0.6153 (mtt180) cc_final: 0.5376 (mmt-90) REVERT: F 607 ASN cc_start: 0.8793 (t0) cc_final: 0.8391 (p0) REVERT: C 91 TYR cc_start: 0.8811 (m-80) cc_final: 0.8127 (m-80) REVERT: D 49 TYR cc_start: 0.8782 (p90) cc_final: 0.8141 (p90) REVERT: D 85 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: H 36 TRP cc_start: 0.7421 (m100) cc_final: 0.7203 (m100) REVERT: H 70 SER cc_start: 0.7911 (t) cc_final: 0.7423 (p) REVERT: H 103 TRP cc_start: 0.7063 (m100) cc_final: 0.6775 (m100) REVERT: L 33 MET cc_start: 0.8093 (tpp) cc_final: 0.7814 (tpp) REVERT: L 42 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7132 (mm-40) REVERT: A 78 ASP cc_start: 0.7545 (t0) cc_final: 0.7293 (t0) REVERT: A 106 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7622 (mt-10) REVERT: A 161 MET cc_start: 0.8592 (tpt) cc_final: 0.8333 (tpt) REVERT: A 217 TYR cc_start: 0.8494 (m-80) cc_final: 0.7964 (m-80) REVERT: M 72 ASP cc_start: 0.8170 (t0) cc_final: 0.7925 (t0) REVERT: M 81 GLN cc_start: 0.8034 (tm130) cc_final: 0.7663 (tm-30) REVERT: N 31 ASN cc_start: 0.8379 (t0) cc_final: 0.7833 (t0) REVERT: N 61 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7477 (ttp80) REVERT: N 79 GLN cc_start: 0.7621 (mp10) cc_final: 0.6856 (tm-30) REVERT: N 82 ASP cc_start: 0.6540 (m-30) cc_final: 0.6323 (m-30) REVERT: J 150 MET cc_start: 0.7542 (mmm) cc_final: 0.7247 (ttm) REVERT: J 166 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.8292 (ttp-110) REVERT: J 440 GLN cc_start: 0.8354 (tp-100) cc_final: 0.7880 (tp-100) REVERT: K 607 ASN cc_start: 0.9076 (t0) cc_final: 0.8828 (t0) REVERT: K 635 ILE cc_start: 0.8954 (tp) cc_final: 0.8376 (tp) outliers start: 51 outliers final: 44 residues processed: 425 average time/residue: 0.1564 time to fit residues: 102.5932 Evaluate side-chains 431 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 386 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 104 LEU 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 195 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 546 SER 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 58 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 51 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 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 158 SER Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 chunk 210 optimal weight: 0.0020 chunk 91 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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** ** C 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** H 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 607 ASN B 652 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3674 r_free = 0.3674 target = 0.133036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103942 restraints weight = 33552.282| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.52 r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 21780 Z= 0.198 Angle : 0.750 58.829 29684 Z= 0.412 Chirality : 0.045 0.686 3497 Planarity : 0.004 0.107 3642 Dihedral : 5.675 51.501 4263 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 2.13 % Allowed : 16.14 % Favored : 81.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2549 helix: 1.37 (0.27), residues: 435 sheet: 0.88 (0.20), residues: 670 loop : -0.27 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 103 TYR 0.030 0.001 TYR N 49 PHE 0.104 0.002 PHE C 67 TRP 0.016 0.001 TRP E 112 HIS 0.010 0.001 HIS M 82A Details of bonding type rmsd covalent geometry : bond 0.00462 (21667) covalent geometry : angle 0.72137 (29386) SS BOND : bond 0.00471 ( 41) SS BOND : angle 1.50131 ( 82) hydrogen bonds : bond 0.03559 ( 616) hydrogen bonds : angle 4.43316 ( 1575) link_ALPHA1-2 : bond 0.01178 ( 3) link_ALPHA1-2 : angle 2.34856 ( 9) link_ALPHA1-3 : bond 0.00800 ( 6) link_ALPHA1-3 : angle 1.42876 ( 18) link_ALPHA1-6 : bond 0.00914 ( 3) link_ALPHA1-6 : angle 1.25803 ( 9) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.41667 ( 45) link_NAG-ASN : bond 0.00459 ( 45) link_NAG-ASN : angle 2.74644 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6055.49 seconds wall clock time: 104 minutes 36.72 seconds (6276.72 seconds total)