Starting phenix.real_space_refine on Tue Jul 23 04:40:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_43190.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_43190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_43190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_43190.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfv_43190/07_2024/8vfv_43190.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 13320 2.51 5 N 3563 2.21 5 O 4224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 27": "OD1" <-> "OD2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 29 Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3451 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "K" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.50, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 9.17 Conformation dependent library (CDL) restraints added in 3.9 seconds 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 38 sheets defined 20.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 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: 6.66 Time building geometry restraints manager: 10.16 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: 96.99 - 104.44: 337 104.44 - 111.89: 10054 111.89 - 119.34: 8375 119.34 - 126.79: 10255 126.79 - 134.23: 365 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 2.520 nonbonded pdb=" OG1 THR A 303 " pdb=" OD1 ASP A 322 " model vdw 1.942 2.440 nonbonded pdb=" O ASN E 197 " pdb=" NH1 ARG A 308 " model vdw 1.997 2.520 nonbonded pdb=" OG SER C 35 " pdb=" O SER C 49 " model vdw 1.999 2.440 nonbonded pdb=" O VAL J 36 " pdb=" OG1 THR K 606 " model vdw 2.051 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 59.710 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.050 ------------------------------------------------------------------------------- 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 21667 Z= 0.433 Angle : 1.197 11.480 29386 Z= 0.685 Chirality : 0.064 0.346 3497 Planarity : 0.009 0.294 3642 Dihedral : 13.913 104.514 8959 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.27 % Allowed : 7.72 % Favored : 92.02 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2549 helix: 0.91 (0.24), residues: 393 sheet: 1.35 (0.18), residues: 757 loop : 0.50 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 479 HIS 0.025 0.003 HIS L 34 PHE 0.030 0.003 PHE E 53 TYR 0.032 0.004 TYR L 87 ARG 0.022 0.001 ARG M 66 *********************** 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 fitting. rotamer outliers: 6 poor density : 516 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.9069 (t) cc_final: 0.8510 (p) REVERT: G 91 TYR cc_start: 0.9072 (m-80) cc_final: 0.8460 (m-80) REVERT: I 103 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7048 (tpp80) REVERT: E 305 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8126 (mtpt) REVERT: E 327 ARG cc_start: 0.5964 (mtt-85) cc_final: 0.5293 (mmt-90) REVERT: F 639 THR cc_start: 0.9236 (m) cc_final: 0.8953 (m) REVERT: C 23 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7346 (ttm110) REVERT: C 75 LYS cc_start: 0.8739 (mttp) cc_final: 0.8121 (tttp) REVERT: A 139 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7180 (mtt90) REVERT: B 638 TYR cc_start: 0.8888 (m-80) cc_final: 0.8458 (m-80) REVERT: N 53 GLN cc_start: 0.7909 (mp10) cc_final: 0.7454 (mp10) REVERT: N 61 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7404 (mtp-110) REVERT: K 625 ASN cc_start: 0.8705 (m-40) cc_final: 0.7932 (t0) REVERT: K 635 ILE cc_start: 0.8892 (tp) cc_final: 0.8675 (tt) REVERT: K 653 GLN cc_start: 0.8516 (tt0) cc_final: 0.8266 (tt0) outliers start: 6 outliers final: 1 residues processed: 521 average time/residue: 0.3314 time to fit residues: 261.9408 Evaluate side-chains 409 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 408 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 GLN E 105 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 428 GLN F 607 ASN A 105 HIS A 114 GLN A 289 ASN A 302 ASN B 607 ASN M 81 GLN J 103 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 425 ASN ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21667 Z= 0.321 Angle : 0.675 13.642 29386 Z= 0.353 Chirality : 0.048 0.199 3497 Planarity : 0.004 0.048 3642 Dihedral : 9.340 75.842 4265 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Rotamer: Outliers : 2.35 % Allowed : 9.89 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 2549 helix: 1.70 (0.27), residues: 411 sheet: 1.33 (0.18), residues: 740 loop : 0.09 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 479 HIS 0.006 0.001 HIS L 34 PHE 0.017 0.002 PHE L 62 TYR 0.020 0.002 TYR J 217 ARG 0.007 0.001 ARG L 50 *********************** 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 463 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 410 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8467 (p) cc_final: 0.8159 (p) REVERT: G 68 THR cc_start: 0.8917 (t) cc_final: 0.8616 (p) REVERT: G 82 MET cc_start: 0.8253 (mtt) cc_final: 0.8021 (mtt) REVERT: E 305 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8335 (mmmt) REVERT: D 50 ASP cc_start: 0.8617 (m-30) cc_final: 0.8410 (m-30) REVERT: H 36 TRP cc_start: 0.7349 (m100) cc_final: 0.7033 (m100) REVERT: H 103 TRP cc_start: 0.7103 (m100) cc_final: 0.6819 (m100) REVERT: L 33 MET cc_start: 0.7874 (tpp) cc_final: 0.7662 (tpp) REVERT: A 139 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7161 (mtt90) REVERT: A 347 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7172 (mttt) REVERT: A 419 ARG cc_start: 0.8404 (mmt90) cc_final: 0.8168 (mmm-85) REVERT: N 79 GLN cc_start: 0.7506 (mp10) cc_final: 0.6846 (tm-30) REVERT: J 111 LEU cc_start: 0.8460 (mt) cc_final: 0.8254 (mt) REVERT: K 632 ASP cc_start: 0.8960 (t0) cc_final: 0.8754 (t0) REVERT: K 635 ILE cc_start: 0.8936 (tp) cc_final: 0.8555 (tt) outliers start: 53 outliers final: 35 residues processed: 443 average time/residue: 0.3344 time to fit residues: 224.7455 Evaluate side-chains 406 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 370 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 248 THR 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 128 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 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 E 249 HIS E 258 GLN E 330 HIS F 607 ASN A 114 GLN B 607 ASN M 3 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN K 585 HIS ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21667 Z= 0.342 Angle : 0.636 10.930 29386 Z= 0.329 Chirality : 0.046 0.210 3497 Planarity : 0.004 0.051 3642 Dihedral : 8.291 69.172 4263 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 3.15 % Allowed : 10.86 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2549 helix: 1.37 (0.26), residues: 429 sheet: 1.23 (0.18), residues: 715 loop : -0.10 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 479 HIS 0.004 0.001 HIS A 249 PHE 0.016 0.002 PHE E 176 TYR 0.030 0.002 TYR N 49 ARG 0.013 0.001 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5098 Ramachandran restraints generated. 2549 Oldfield, 0 Emsley, 2549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 390 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8426 (p) cc_final: 0.8099 (p) REVERT: G 68 THR cc_start: 0.8908 (t) cc_final: 0.8572 (p) REVERT: D 49 TYR cc_start: 0.8977 (p90) cc_final: 0.8666 (p90) REVERT: D 50 ASP cc_start: 0.8837 (m-30) cc_final: 0.8593 (m-30) REVERT: D 85 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: H 36 TRP cc_start: 0.7296 (m100) cc_final: 0.6887 (m-90) REVERT: H 103 TRP cc_start: 0.7105 (m100) cc_final: 0.6803 (m100) REVERT: A 139 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7196 (mtt90) REVERT: A 217 TYR cc_start: 0.8893 (m-80) cc_final: 0.8356 (m-80) REVERT: B 607 ASN cc_start: 0.9071 (t0) cc_final: 0.8822 (t0) REVERT: B 632 ASP cc_start: 0.9182 (t0) cc_final: 0.8957 (t0) REVERT: M 72 ASP cc_start: 0.8114 (t0) cc_final: 0.7886 (t0) REVERT: M 91 TYR cc_start: 0.8746 (m-80) cc_final: 0.8420 (m-80) REVERT: N 45 LYS cc_start: 0.8618 (tttp) cc_final: 0.8374 (tttm) REVERT: J 111 LEU cc_start: 0.8449 (mt) cc_final: 0.8200 (mt) REVERT: K 621 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7519 (mt-10) REVERT: K 635 ILE cc_start: 0.8938 (tp) cc_final: 0.8419 (tp) outliers start: 71 outliers final: 50 residues processed: 431 average time/residue: 0.3312 time to fit residues: 217.4043 Evaluate side-chains 419 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 368 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain D residue 26 THR 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 D residue 102 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 61 ASP 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 M residue 110 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 247 CYS Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain J residue 442 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 53 GLN E 330 HIS D 31 ASN A 114 GLN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.005 0.063 21667 Z= 0.332 Angle : 0.610 11.688 29386 Z= 0.313 Chirality : 0.046 0.226 3497 Planarity : 0.004 0.054 3642 Dihedral : 7.705 62.690 4263 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 3.10 % Allowed : 12.20 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2549 helix: 1.27 (0.26), residues: 429 sheet: 1.04 (0.19), residues: 722 loop : -0.24 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 479 HIS 0.005 0.001 HIS E 249 PHE 0.013 0.002 PHE E 176 TYR 0.023 0.002 TYR N 49 ARG 0.005 0.000 ARG M 23 *********************** 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 453 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 383 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8385 (p) cc_final: 0.8077 (p) REVERT: G 68 THR cc_start: 0.8885 (t) cc_final: 0.8559 (p) REVERT: F 584 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 23 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7903 (ttm110) REVERT: H 25 SER cc_start: 0.6432 (m) cc_final: 0.5880 (t) REVERT: H 36 TRP cc_start: 0.7438 (m100) cc_final: 0.6996 (m100) REVERT: H 89 VAL cc_start: 0.6052 (OUTLIER) cc_final: 0.5840 (m) REVERT: H 103 TRP cc_start: 0.7125 (m100) cc_final: 0.6771 (m100) REVERT: L 98 PHE cc_start: 0.8167 (m-80) cc_final: 0.7604 (m-80) REVERT: A 308 ARG cc_start: 0.7998 (mpp80) cc_final: 0.7694 (mtt90) REVERT: B 632 ASP cc_start: 0.9174 (t0) cc_final: 0.8920 (t0) REVERT: M 72 ASP cc_start: 0.8035 (t0) cc_final: 0.7804 (t0) REVERT: N 45 LYS cc_start: 0.8597 (tttp) cc_final: 0.8355 (tttm) REVERT: N 61 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7593 (mtm110) REVERT: N 79 GLN cc_start: 0.7629 (mp10) cc_final: 0.7135 (mp10) REVERT: N 103 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7737 (mmm160) REVERT: K 635 ILE cc_start: 0.8956 (tp) cc_final: 0.8439 (tp) outliers start: 70 outliers final: 51 residues processed: 419 average time/residue: 0.3326 time to fit residues: 213.5922 Evaluate side-chains 416 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 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 103 GLN Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 61 ASP 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 M residue 110 THR 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 442 VAL Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 40.0000 chunk 210 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN I 17 GLN I 53 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 607 ASN D 31 ASN A 114 GLN B 607 ASN M 81 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21667 Z= 0.297 Angle : 0.580 11.811 29386 Z= 0.298 Chirality : 0.045 0.221 3497 Planarity : 0.004 0.054 3642 Dihedral : 7.220 56.478 4263 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 13.44 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2549 helix: 1.28 (0.27), residues: 429 sheet: 0.80 (0.19), residues: 716 loop : -0.26 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS E 249 PHE 0.014 0.002 PHE H 78 TYR 0.029 0.002 TYR N 49 ARG 0.006 0.000 ARG B 542 *********************** 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 fitting. rotamer outliers: 70 poor density : 383 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8329 (p) cc_final: 0.8050 (p) REVERT: G 68 THR cc_start: 0.8859 (t) cc_final: 0.8550 (p) REVERT: G 81 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (mm110) REVERT: F 584 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8368 (mt-10) REVERT: D 85 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: H 25 SER cc_start: 0.6473 (m) cc_final: 0.6147 (t) REVERT: H 36 TRP cc_start: 0.7521 (m100) cc_final: 0.7140 (m100) REVERT: H 89 VAL cc_start: 0.6023 (OUTLIER) cc_final: 0.5808 (m) REVERT: H 103 TRP cc_start: 0.7104 (m100) cc_final: 0.6744 (m100) REVERT: L 24 ARG cc_start: 0.8116 (mpt180) cc_final: 0.7853 (mmt-90) REVERT: L 98 PHE cc_start: 0.8265 (m-80) cc_final: 0.7765 (m-80) REVERT: A 78 ASP cc_start: 0.7324 (t0) cc_final: 0.6996 (t0) REVERT: A 106 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7459 (mt-10) REVERT: A 308 ARG cc_start: 0.7987 (mpp80) cc_final: 0.7710 (mtt90) REVERT: A 426 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (mtt) REVERT: B 632 ASP cc_start: 0.9186 (t0) cc_final: 0.8905 (t0) REVERT: M 72 ASP cc_start: 0.8006 (t0) cc_final: 0.7773 (t0) REVERT: M 81 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7750 (tm-30) REVERT: N 45 LYS cc_start: 0.8565 (tttp) cc_final: 0.8327 (tttm) REVERT: J 414 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7653 (tt) REVERT: K 591 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8838 (tt0) REVERT: K 635 ILE cc_start: 0.8952 (tp) cc_final: 0.8431 (tp) outliers start: 70 outliers final: 51 residues processed: 416 average time/residue: 0.3470 time to fit residues: 222.5421 Evaluate side-chains 425 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 369 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL 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 247 CYS Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 58 VAL 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 89 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 426 MET 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 61 ASP Chi-restraints excluded: chain M residue 62 SER 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 M residue 110 THR 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 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.3980 chunk 221 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 330 HIS D 31 ASN A 114 GLN A 216 HIS B 607 ASN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21667 Z= 0.293 Angle : 0.574 10.922 29386 Z= 0.294 Chirality : 0.045 0.216 3497 Planarity : 0.004 0.055 3642 Dihedral : 6.889 59.930 4263 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 3.77 % Allowed : 13.48 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2549 helix: 1.29 (0.27), residues: 429 sheet: 0.77 (0.19), residues: 711 loop : -0.33 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.003 0.001 HIS E 249 PHE 0.017 0.002 PHE E 53 TYR 0.026 0.001 TYR N 49 ARG 0.006 0.000 ARG M 23 *********************** 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 464 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 379 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 28 THR cc_start: 0.8336 (p) cc_final: 0.8073 (p) REVERT: G 68 THR cc_start: 0.8860 (t) cc_final: 0.8553 (p) REVERT: G 81 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (mm110) REVERT: D 50 ASP cc_start: 0.8742 (m-30) cc_final: 0.8398 (m-30) REVERT: D 85 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: H 25 SER cc_start: 0.6614 (m) cc_final: 0.6122 (t) REVERT: H 36 TRP cc_start: 0.7566 (m100) cc_final: 0.7192 (m100) REVERT: H 89 VAL cc_start: 0.6014 (OUTLIER) cc_final: 0.5786 (m) REVERT: H 103 TRP cc_start: 0.7079 (m100) cc_final: 0.6652 (m100) REVERT: L 33 MET cc_start: 0.8134 (tpp) cc_final: 0.7826 (tpp) REVERT: A 78 ASP cc_start: 0.7316 (t0) cc_final: 0.6987 (t0) REVERT: A 106 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7493 (mt-10) REVERT: A 308 ARG cc_start: 0.7942 (mpp80) cc_final: 0.7480 (mtt90) REVERT: A 419 ARG cc_start: 0.8433 (mmt90) cc_final: 0.8122 (mmm-85) REVERT: A 426 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: B 632 ASP cc_start: 0.9191 (t0) cc_final: 0.8948 (t0) REVERT: M 72 ASP cc_start: 0.8045 (t0) cc_final: 0.7821 (t0) REVERT: N 45 LYS cc_start: 0.8566 (tttp) cc_final: 0.8322 (tttm) REVERT: J 414 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7654 (tt) REVERT: K 591 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8853 (tt0) REVERT: K 635 ILE cc_start: 0.8931 (tp) cc_final: 0.8401 (tp) outliers start: 85 outliers final: 63 residues processed: 425 average time/residue: 0.3362 time to fit residues: 219.9914 Evaluate side-chains 435 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 367 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 426 MET 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 61 ASP Chi-restraints excluded: chain M residue 62 SER 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 M residue 110 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 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 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS D 31 ASN A 114 GLN B 607 ASN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21667 Z= 0.239 Angle : 0.556 12.388 29386 Z= 0.285 Chirality : 0.044 0.293 3497 Planarity : 0.004 0.053 3642 Dihedral : 6.418 59.173 4263 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2549 helix: 1.32 (0.27), residues: 435 sheet: 0.74 (0.19), residues: 713 loop : -0.35 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.003 0.001 HIS H 53 PHE 0.017 0.002 PHE L 71 TYR 0.026 0.001 TYR N 49 ARG 0.006 0.000 ARG M 23 *********************** 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 466 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 389 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 TYR cc_start: 0.8755 (p90) cc_final: 0.8471 (p90) REVERT: G 68 THR cc_start: 0.8877 (t) cc_final: 0.8582 (p) REVERT: G 81 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8538 (mm110) REVERT: G 82 MET cc_start: 0.8328 (mtt) cc_final: 0.7697 (mtm) REVERT: D 47 MET cc_start: 0.8441 (mmt) cc_final: 0.8071 (mmt) REVERT: D 49 TYR cc_start: 0.8866 (p90) cc_final: 0.7922 (p90) REVERT: D 50 ASP cc_start: 0.8685 (m-30) cc_final: 0.8230 (m-30) REVERT: D 85 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: H 25 SER cc_start: 0.6580 (m) cc_final: 0.6218 (t) REVERT: H 36 TRP cc_start: 0.7603 (m100) cc_final: 0.7242 (m100) REVERT: H 89 VAL cc_start: 0.5998 (OUTLIER) cc_final: 0.5771 (m) REVERT: H 103 TRP cc_start: 0.7025 (m100) cc_final: 0.6652 (m100) REVERT: L 33 MET cc_start: 0.8171 (tpp) cc_final: 0.7880 (tpp) REVERT: L 88 CYS cc_start: 0.5083 (p) cc_final: 0.4875 (p) REVERT: A 78 ASP cc_start: 0.7379 (t0) cc_final: 0.7078 (t0) REVERT: A 106 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7465 (mt-10) REVERT: A 161 MET cc_start: 0.8511 (tpt) cc_final: 0.8294 (tpt) REVERT: A 217 TYR cc_start: 0.8849 (m-80) cc_final: 0.8143 (m-80) REVERT: A 308 ARG cc_start: 0.7909 (mpp80) cc_final: 0.7471 (mtt90) REVERT: B 632 ASP cc_start: 0.9165 (t0) cc_final: 0.8916 (t0) REVERT: M 72 ASP cc_start: 0.8067 (t0) cc_final: 0.7824 (t0) REVERT: N 45 LYS cc_start: 0.8553 (tttp) cc_final: 0.8315 (tttm) REVERT: J 414 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7663 (tt) REVERT: K 591 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8872 (tt0) REVERT: K 635 ILE cc_start: 0.8896 (tp) cc_final: 0.8358 (tp) outliers start: 77 outliers final: 57 residues processed: 427 average time/residue: 0.3241 time to fit residues: 212.5553 Evaluate side-chains 436 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 375 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain J residue 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 296 CYS Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 167 optimal weight: 0.0870 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 13 GLN G 76 ASN I 17 GLN D 31 ASN A 114 GLN B 607 ASN B 652 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21667 Z= 0.196 Angle : 0.530 10.412 29386 Z= 0.274 Chirality : 0.043 0.218 3497 Planarity : 0.004 0.052 3642 Dihedral : 5.932 53.778 4263 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 3.24 % Allowed : 14.59 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2549 helix: 1.40 (0.27), residues: 435 sheet: 0.79 (0.20), residues: 670 loop : -0.37 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.005 0.001 HIS H 53 PHE 0.017 0.001 PHE L 71 TYR 0.029 0.001 TYR N 49 ARG 0.006 0.000 ARG N 61 *********************** 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 470 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 397 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 TYR cc_start: 0.8672 (p90) cc_final: 0.8466 (p90) REVERT: G 68 THR cc_start: 0.8898 (t) cc_final: 0.8563 (p) REVERT: G 81 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (mm110) REVERT: G 82 MET cc_start: 0.8221 (mtt) cc_final: 0.7573 (mtm) REVERT: H 25 SER cc_start: 0.6632 (m) cc_final: 0.6396 (t) REVERT: H 36 TRP cc_start: 0.7539 (m100) cc_final: 0.7288 (m100) REVERT: H 103 TRP cc_start: 0.6977 (m100) cc_final: 0.6591 (m100) REVERT: L 33 MET cc_start: 0.8151 (tpp) cc_final: 0.7828 (tpp) REVERT: L 88 CYS cc_start: 0.4900 (p) cc_final: 0.4691 (p) REVERT: A 78 ASP cc_start: 0.7363 (t0) cc_final: 0.7072 (t0) REVERT: A 106 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7454 (mt-10) REVERT: A 217 TYR cc_start: 0.8794 (m-80) cc_final: 0.8175 (m-80) REVERT: B 632 ASP cc_start: 0.9155 (t0) cc_final: 0.8919 (t0) REVERT: M 72 ASP cc_start: 0.8040 (t0) cc_final: 0.7819 (t0) REVERT: M 81 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7883 (tp-100) REVERT: N 45 LYS cc_start: 0.8541 (tttp) cc_final: 0.8310 (tttm) REVERT: N 79 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7433 (mm110) REVERT: K 591 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8899 (tt0) REVERT: K 635 ILE cc_start: 0.8905 (tp) cc_final: 0.8367 (tp) outliers start: 73 outliers final: 52 residues processed: 439 average time/residue: 0.3161 time to fit residues: 214.7074 Evaluate side-chains 439 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 385 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 76 ASN 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 19 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 79 GLN 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 296 CYS Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 179 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN H 39 GLN L 38 GLN A 114 GLN B 607 ASN B 652 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21667 Z= 0.209 Angle : 0.534 9.774 29386 Z= 0.275 Chirality : 0.043 0.214 3497 Planarity : 0.004 0.051 3642 Dihedral : 5.826 52.608 4263 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 2.88 % Allowed : 15.79 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2549 helix: 1.54 (0.27), residues: 417 sheet: 0.78 (0.20), residues: 670 loop : -0.35 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 479 HIS 0.004 0.001 HIS H 53 PHE 0.019 0.001 PHE J 361 TYR 0.028 0.001 TYR N 49 ARG 0.008 0.000 ARG N 61 *********************** 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 454 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 389 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.8894 (t) cc_final: 0.8564 (p) REVERT: G 81 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8529 (mm110) REVERT: D 85 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: H 36 TRP cc_start: 0.7578 (m100) cc_final: 0.7330 (m100) REVERT: H 103 TRP cc_start: 0.6987 (m100) cc_final: 0.6594 (m100) REVERT: L 33 MET cc_start: 0.8158 (tpp) cc_final: 0.7811 (tpp) REVERT: L 88 CYS cc_start: 0.4881 (p) cc_final: 0.4666 (p) REVERT: A 78 ASP cc_start: 0.7373 (t0) cc_final: 0.7126 (t0) REVERT: A 106 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7469 (mt-10) REVERT: A 125 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 217 TYR cc_start: 0.8740 (m-80) cc_final: 0.8088 (m-80) REVERT: B 632 ASP cc_start: 0.9160 (t0) cc_final: 0.8926 (t0) REVERT: M 72 ASP cc_start: 0.8028 (t0) cc_final: 0.7804 (t0) REVERT: M 81 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7880 (tp-100) REVERT: M 105 GLN cc_start: 0.8235 (mm110) cc_final: 0.7977 (mm110) REVERT: N 45 LYS cc_start: 0.8599 (tttp) cc_final: 0.8342 (tttm) REVERT: N 79 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7456 (mm110) REVERT: K 591 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8875 (tt0) REVERT: K 635 ILE cc_start: 0.8885 (tp) cc_final: 0.8344 (tp) outliers start: 65 outliers final: 56 residues processed: 423 average time/residue: 0.3248 time to fit residues: 211.6347 Evaluate side-chains 443 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 383 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER 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 89 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL 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 37 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 79 GLN 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 296 CYS Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 D 31 ASN A 114 GLN B 607 ASN B 652 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 21667 Z= 0.247 Angle : 0.687 59.141 29386 Z= 0.388 Chirality : 0.044 0.454 3497 Planarity : 0.004 0.075 3642 Dihedral : 5.842 52.614 4263 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 2.88 % Allowed : 15.52 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2549 helix: 1.53 (0.27), residues: 417 sheet: 0.78 (0.20), residues: 670 loop : -0.36 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 479 HIS 0.004 0.001 HIS A 216 PHE 0.017 0.001 PHE J 361 TYR 0.026 0.001 TYR N 49 ARG 0.009 0.000 ARG M 66 ********************** 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 450 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 385 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 THR cc_start: 0.8895 (t) cc_final: 0.8563 (p) REVERT: G 81 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8531 (mm110) REVERT: D 31 ASN cc_start: 0.8654 (p0) cc_final: 0.8372 (p0) REVERT: D 47 MET cc_start: 0.8411 (mmt) cc_final: 0.7894 (mmt) REVERT: D 85 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: H 36 TRP cc_start: 0.7574 (m100) cc_final: 0.7328 (m100) REVERT: H 103 TRP cc_start: 0.6987 (m100) cc_final: 0.6592 (m100) REVERT: L 33 MET cc_start: 0.8152 (tpp) cc_final: 0.7810 (tpp) REVERT: L 88 CYS cc_start: 0.4878 (p) cc_final: 0.4662 (p) REVERT: A 78 ASP cc_start: 0.7375 (t0) cc_final: 0.7125 (t0) REVERT: A 106 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7457 (mt-10) REVERT: A 125 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (mm) REVERT: A 217 TYR cc_start: 0.8738 (m-80) cc_final: 0.8088 (m-80) REVERT: B 632 ASP cc_start: 0.9160 (t0) cc_final: 0.8926 (t0) REVERT: M 72 ASP cc_start: 0.8022 (t0) cc_final: 0.7802 (t0) REVERT: M 81 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7880 (tp-100) REVERT: M 105 GLN cc_start: 0.8219 (mm110) cc_final: 0.7959 (mm110) REVERT: N 45 LYS cc_start: 0.8608 (tttp) cc_final: 0.8357 (tttm) REVERT: N 79 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7458 (mm110) REVERT: K 591 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8876 (tt0) REVERT: K 635 ILE cc_start: 0.8884 (tp) cc_final: 0.8342 (tp) outliers start: 65 outliers final: 59 residues processed: 418 average time/residue: 0.3187 time to fit residues: 204.5966 Evaluate side-chains 445 residues out of total 2255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 382 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 98 SER 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 89 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 346 VAL 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 37 VAL Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 82 HIS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 79 GLN 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 296 CYS Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 443 ILE Chi-restraints excluded: chain J residue 467 THR Chi-restraints excluded: chain J residue 475 MET Chi-restraints excluded: chain K residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 202 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 607 ASN B 652 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 591 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 = 0.3659 r_free = 0.3659 target = 0.132253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102429 restraints weight = 33754.639| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.56 r_work: 0.3117 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 21667 Z= 0.247 Angle : 0.687 59.141 29386 Z= 0.388 Chirality : 0.044 0.454 3497 Planarity : 0.004 0.075 3642 Dihedral : 5.842 52.614 4263 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 2.84 % Allowed : 15.57 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2549 helix: 1.53 (0.27), residues: 417 sheet: 0.78 (0.20), residues: 670 loop : -0.36 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 479 HIS 0.004 0.001 HIS A 216 PHE 0.017 0.001 PHE J 361 TYR 0.026 0.001 TYR N 49 ARG 0.009 0.000 ARG M 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.18 seconds wall clock time: 93 minutes 38.03 seconds (5618.03 seconds total)