Starting phenix.real_space_refine on Thu Jan 23 16:12:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.map" model { file = "/net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orq_20178/01_2025/6orq_20178.cif" } resolution = 4.4 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= 0.144 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 132 5.16 5 C 12626 2.51 5 N 3364 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "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: "c" 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: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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: "h" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.02, per 1000 atoms: 0.60 Number of scatterers: 20176 At special positions: 0 Unit cell: (146.472, 145.036, 162.268, 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 132 16.00 O 4054 8.00 N 3364 7.00 C 12626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.07 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 160 " " NAG B 615 " - " ASN B 295 " " NAG B 616 " - " ASN B 301 " " NAG B 619 " - " ASN B 339 " " NAG B 620 " - " ASN B 355 " " NAG B 623 " - " ASN B 392 " " NAG B 624 " - " ASN B 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 611 " - " ASN G 295 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 621 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 614 " - " ASN I 295 " " NAG I 615 " - " ASN I 301 " " NAG I 619 " - " ASN I 339 " " NAG I 620 " - " ASN I 355 " " NAG I 623 " - " ASN I 392 " " NAG M 1 " - " ASN B 197 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 332 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 234 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 279 " " NAG W 1 " - " ASN G 301 " " NAG X 1 " - " ASN G 332 " " NAG Y 1 " - " ASN G 386 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN I 197 " " NAG c 1 " - " ASN I 234 " " NAG d 1 " - " ASN I 262 " " NAG e 1 " - " ASN I 279 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 386 " " NAG h 1 " - " ASN I 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.6 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 51 sheets defined 20.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.965A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.757A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.876A pdb=" N ILE B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.536A pdb=" N ASN B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.513A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.997A pdb=" N VAL B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.668A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.771A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.742A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 59 through 64 removed outlier: 3.908A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.554A pdb=" N ASN G 137 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.522A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 4.280A pdb=" N GLY G 354 " --> pdb=" O LYS G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.570A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.940A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.796A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.777A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 3.552A pdb=" N ASN I 137 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.503A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.259A pdb=" N GLY I 354 " --> pdb=" O LYS I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 368 through 372 removed outlier: 4.028A pdb=" N VAL I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.974A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.877A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 35 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.818A pdb=" N LYS B 490 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 4.046A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.582A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 286 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 297 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.533A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.601A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.949A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.973A pdb=" N SER E 63 " --> pdb=" O ASN E 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.908A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.524A pdb=" N LYS G 46 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS G 490 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 130 through 132 removed outlier: 4.057A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR G 132 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AD1, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.731A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.678A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 394 through 395 removed outlier: 3.597A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.737A pdb=" N LYS I 490 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.790A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.087A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.947A pdb=" N LEU I 122 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 132 removed outlier: 4.110A pdb=" N GLN I 130 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.574A pdb=" N GLN I 287 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.741A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.553A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AE9, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER K 63 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AF5, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'L' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER L 63 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 415 hydrogen bonds defined for protein. 1026 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: 6.72 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3261 1.31 - 1.45: 5847 1.45 - 1.58: 11293 1.58 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 20587 Sorted by residual: bond pdb=" C3 NAG a 1 " pdb=" C4 NAG a 1 " ideal model delta sigma weight residual 1.524 1.449 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 NAG a 1 " pdb=" C5 NAG a 1 " ideal model delta sigma weight residual 1.532 1.463 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 NAG a 2 " pdb=" C4 NAG a 2 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 NAG a 1 " pdb=" C8 NAG a 1 " ideal model delta sigma weight residual 1.509 1.443 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 20582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 27272 3.58 - 7.16: 552 7.16 - 10.75: 92 10.75 - 14.33: 9 14.33 - 17.91: 9 Bond angle restraints: 27934 Sorted by residual: angle pdb=" N LEU J 45 " pdb=" CA LEU J 45 " pdb=" C LEU J 45 " ideal model delta sigma weight residual 110.80 125.23 -14.43 2.13e+00 2.20e-01 4.59e+01 angle pdb=" N LEU H 45 " pdb=" CA LEU H 45 " pdb=" C LEU H 45 " ideal model delta sigma weight residual 110.80 125.22 -14.42 2.13e+00 2.20e-01 4.58e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 110.80 125.19 -14.39 2.13e+00 2.20e-01 4.57e+01 angle pdb=" C3 NAG a 1 " pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " ideal model delta sigma weight residual 110.74 92.83 17.91 3.00e+00 1.11e-01 3.56e+01 angle pdb=" N VAL B 371 " pdb=" CA VAL B 371 " pdb=" C VAL B 371 " ideal model delta sigma weight residual 113.42 106.98 6.44 1.17e+00 7.31e-01 3.03e+01 ... (remaining 27929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12478 22.12 - 44.23: 703 44.23 - 66.35: 116 66.35 - 88.47: 74 88.47 - 110.59: 31 Dihedral angle restraints: 13402 sinusoidal: 6382 harmonic: 7020 Sorted by residual: dihedral pdb=" CA LYS J 13 " pdb=" C LYS J 13 " pdb=" N PRO J 14 " pdb=" CA PRO J 14 " ideal model delta harmonic sigma weight residual 180.00 -123.10 -56.90 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -123.14 -56.86 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3213 0.166 - 0.333: 109 0.333 - 0.499: 11 0.499 - 0.666: 0 0.666 - 0.832: 4 Chirality restraints: 3337 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C5 NAG a 1 " pdb=" C4 NAG a 1 " pdb=" C6 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.58 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3334 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.404 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" C7 NAG a 2 " 0.166 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.243 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " 0.366 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG a 1 " -0.127 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO D 14 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.053 5.00e-02 4.00e+02 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 297 2.61 - 3.18: 17193 3.18 - 3.76: 30218 3.76 - 4.33: 37608 4.33 - 4.90: 59246 Nonbonded interactions: 144562 Sorted by model distance: nonbonded pdb=" O4 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.039 3.040 nonbonded pdb=" O4 NAG a 1 " pdb=" O6 NAG a 1 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR J 68 " pdb=" O GLN J 81 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR H 68 " pdb=" O GLN H 81 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR D 68 " pdb=" O GLN D 81 " model vdw 2.243 3.040 ... (remaining 144557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 31 through 505 or resid 601 through 619)) selection = chain 'G' selection = (chain 'I' and (resid 31 through 505 or resid 601 through 619)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'f' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.190 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.180 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.008 0.075 20587 Z= 0.519 Angle : 1.309 17.910 27934 Z= 0.668 Chirality : 0.077 0.832 3337 Planarity : 0.011 0.332 3463 Dihedral : 15.528 110.585 8809 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.29 % Favored : 83.38 % Rotamer: Outliers : 1.04 % Allowed : 7.81 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.61 % 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: -4.97 (0.13), residues: 2388 helix: -4.26 (0.15), residues: 288 sheet: -2.27 (0.23), residues: 459 loop : -3.69 (0.12), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP I 35 HIS 0.013 0.003 HIS E 76 PHE 0.023 0.003 PHE L 98 TYR 0.037 0.004 TYR I 134 ARG 0.015 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 618 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 GLN cc_start: 0.8982 (mp-120) cc_final: 0.8722 (mp10) REVERT: A 574 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: A 584 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 588 ARG cc_start: 0.9131 (ttt180) cc_final: 0.8893 (ttt90) REVERT: A 621 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 647 GLU cc_start: 0.9051 (pp20) cc_final: 0.8847 (pp20) REVERT: A 648 GLU cc_start: 0.9036 (pp20) cc_final: 0.8704 (pp20) REVERT: A 654 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8771 (tp30) REVERT: B 80 ASN cc_start: 0.8902 (t0) cc_final: 0.8443 (p0) REVERT: B 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8596 (ttm) REVERT: B 114 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9049 (tm-30) REVERT: B 161 MET cc_start: 0.9228 (tpp) cc_final: 0.8837 (tpp) REVERT: B 256 SER cc_start: 0.9266 (m) cc_final: 0.9012 (m) REVERT: B 340 GLU cc_start: 0.9317 (tp30) cc_final: 0.9109 (tp30) REVERT: C 535 MET cc_start: 0.8927 (mtt) cc_final: 0.8591 (mmm) REVERT: C 542 ARG cc_start: 0.9260 (mtp-110) cc_final: 0.9004 (ttp80) REVERT: C 543 ASN cc_start: 0.8918 (t0) cc_final: 0.8642 (t0) REVERT: C 574 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (ttmm) REVERT: C 584 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 621 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 648 GLU cc_start: 0.9151 (pp20) cc_final: 0.8713 (pm20) REVERT: D 34 MET cc_start: 0.9026 (mpt) cc_final: 0.8790 (mmm) REVERT: D 36 TRP cc_start: 0.8331 (m100) cc_final: 0.8021 (m-10) REVERT: D 82 LEU cc_start: 0.9165 (mt) cc_final: 0.8760 (mt) REVERT: D 85 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8472 (pp20) REVERT: E 37 GLN cc_start: 0.7675 (pp30) cc_final: 0.7095 (pp30) REVERT: E 38 GLN cc_start: 0.8843 (pt0) cc_final: 0.8463 (pt0) REVERT: E 47 LEU cc_start: 0.8909 (mm) cc_final: 0.8702 (mm) REVERT: E 72 THR cc_start: 0.7080 (t) cc_final: 0.6755 (t) REVERT: F 574 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (ttmm) REVERT: F 584 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 621 GLU cc_start: 0.8845 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 622 ILE cc_start: 0.9196 (pp) cc_final: 0.7980 (pp) REVERT: F 624 ASP cc_start: 0.8804 (m-30) cc_final: 0.8535 (m-30) REVERT: F 648 GLU cc_start: 0.9104 (pp20) cc_final: 0.8833 (pp20) REVERT: F 654 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8724 (tp30) REVERT: F 655 LYS cc_start: 0.8833 (pptt) cc_final: 0.8614 (pptt) REVERT: G 114 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9115 (tm-30) REVERT: G 150 MET cc_start: 0.8892 (tmt) cc_final: 0.8540 (tmm) REVERT: G 161 MET cc_start: 0.9127 (tpp) cc_final: 0.8759 (tpp) REVERT: G 252 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8993 (mtpp) REVERT: G 302 ASN cc_start: 0.8304 (t0) cc_final: 0.7879 (t0) REVERT: G 321 ASP cc_start: 0.8678 (t70) cc_final: 0.8301 (t70) REVERT: H 1 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8388 (pm20) REVERT: H 29 PHE cc_start: 0.8894 (t80) cc_final: 0.8578 (t80) REVERT: H 51 ILE cc_start: 0.8556 (pt) cc_final: 0.8301 (pt) REVERT: H 67 PHE cc_start: 0.8728 (p90) cc_final: 0.8352 (p90) REVERT: I 80 ASN cc_start: 0.9034 (t0) cc_final: 0.8608 (p0) REVERT: I 114 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9090 (tm-30) REVERT: I 125 LEU cc_start: 0.8971 (tt) cc_final: 0.8673 (tt) REVERT: I 211 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8747 (tm-30) REVERT: I 217 TYR cc_start: 0.8111 (m-10) cc_final: 0.7025 (m-10) REVERT: I 230 ASP cc_start: 0.8785 (t0) cc_final: 0.8570 (t0) REVERT: I 252 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8941 (mtpp) REVERT: I 340 GLU cc_start: 0.9287 (tp30) cc_final: 0.9015 (tm-30) REVERT: I 425 ASN cc_start: 0.9354 (p0) cc_final: 0.9113 (p0) REVERT: I 452 LEU cc_start: 0.9181 (mm) cc_final: 0.8443 (tt) REVERT: I 477 ASP cc_start: 0.9278 (p0) cc_final: 0.9070 (p0) REVERT: I 479 TRP cc_start: 0.8841 (m-10) cc_final: 0.8452 (m-10) REVERT: I 482 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8633 (mm-30) REVERT: J 1 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8244 (pm20) REVERT: J 27 PHE cc_start: 0.8394 (m-10) cc_final: 0.8031 (m-10) REVERT: J 29 PHE cc_start: 0.8710 (t80) cc_final: 0.8480 (t80) REVERT: J 34 MET cc_start: 0.9346 (mpt) cc_final: 0.9105 (mmm) REVERT: J 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7883 (m100) REVERT: J 71 ARG cc_start: 0.8473 (tmt90) cc_final: 0.8155 (ttt-90) REVERT: J 82 LEU cc_start: 0.8863 (mt) cc_final: 0.8015 (mt) REVERT: J 85 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8314 (pp20) REVERT: J 91 TYR cc_start: 0.8743 (m-80) cc_final: 0.8533 (m-80) REVERT: K 37 GLN cc_start: 0.8014 (pp30) cc_final: 0.7190 (pp30) REVERT: K 38 GLN cc_start: 0.8597 (pt0) cc_final: 0.8307 (pp30) REVERT: K 45 LYS cc_start: 0.8632 (tptm) cc_final: 0.8255 (ttpt) REVERT: K 81 GLU cc_start: 0.9277 (pp20) cc_final: 0.8967 (pp20) REVERT: L 37 GLN cc_start: 0.8466 (pp30) cc_final: 0.7784 (pp30) REVERT: L 38 GLN cc_start: 0.8651 (pt0) cc_final: 0.8305 (pp30) REVERT: L 45 LYS cc_start: 0.8997 (tptm) cc_final: 0.8638 (ttpt) outliers start: 22 outliers final: 10 residues processed: 629 average time/residue: 0.3365 time to fit residues: 316.0766 Evaluate side-chains 433 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 420 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 590 GLN A 651 ASN B 66 HIS B 203 GLN C 570 HIS C 590 GLN C 616 ASN C 651 ASN D 81 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 590 GLN F 616 ASN F 651 ASN G 66 HIS G 293 GLN G 300 ASN G 440 GLN H 81 GLN I 258 GLN J 81 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.071874 restraints weight = 63373.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.074277 restraints weight = 33425.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.075892 restraints weight = 21525.277| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20587 Z= 0.205 Angle : 0.896 18.798 27934 Z= 0.432 Chirality : 0.054 0.469 3337 Planarity : 0.006 0.091 3463 Dihedral : 13.060 97.729 4330 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.11 % Favored : 86.68 % Rotamer: Outliers : 0.43 % Allowed : 4.07 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.35 % 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: -4.34 (0.14), residues: 2388 helix: -2.53 (0.21), residues: 336 sheet: -1.44 (0.26), residues: 408 loop : -3.63 (0.12), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 427 HIS 0.010 0.002 HIS K 76 PHE 0.019 0.001 PHE B 376 TYR 0.024 0.002 TYR G 134 ARG 0.005 0.001 ARG I 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 598 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8767 (mmt) cc_final: 0.8544 (mmm) REVERT: A 584 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 617 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8057 (mtm-85) REVERT: A 621 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 622 ILE cc_start: 0.9097 (pt) cc_final: 0.8870 (mp) REVERT: A 626 MET cc_start: 0.8352 (mtm) cc_final: 0.7262 (mtt) REVERT: A 648 GLU cc_start: 0.9132 (pp20) cc_final: 0.8806 (pp20) REVERT: B 80 ASN cc_start: 0.8936 (t0) cc_final: 0.8402 (p0) REVERT: B 98 ASN cc_start: 0.8564 (t0) cc_final: 0.7581 (t0) REVERT: B 99 ASN cc_start: 0.9179 (m-40) cc_final: 0.8909 (m-40) REVERT: B 114 GLN cc_start: 0.9322 (tm-30) cc_final: 0.9061 (tm-30) REVERT: B 161 MET cc_start: 0.9176 (tpp) cc_final: 0.8911 (tpp) REVERT: B 211 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8787 (tm-30) REVERT: B 321 ASP cc_start: 0.8958 (t70) cc_final: 0.8468 (t0) REVERT: B 452 LEU cc_start: 0.9407 (pt) cc_final: 0.8849 (pp) REVERT: B 475 MET cc_start: 0.7604 (tmm) cc_final: 0.7223 (tmm) REVERT: C 584 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8547 (tm-30) REVERT: C 617 ARG cc_start: 0.8610 (mtt180) cc_final: 0.7887 (mtm180) REVERT: C 621 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8258 (tm-30) REVERT: C 622 ILE cc_start: 0.9098 (pt) cc_final: 0.8850 (mp) REVERT: C 626 MET cc_start: 0.8349 (mtm) cc_final: 0.7663 (mtm) REVERT: C 648 GLU cc_start: 0.9115 (pp20) cc_final: 0.8635 (pm20) REVERT: C 654 GLU cc_start: 0.8902 (tp30) cc_final: 0.8496 (tp30) REVERT: D 1 GLU cc_start: 0.6711 (pm20) cc_final: 0.6199 (pm20) REVERT: D 34 MET cc_start: 0.9220 (mpp) cc_final: 0.9011 (mmm) REVERT: D 39 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8402 (mm110) REVERT: D 82 MET cc_start: 0.8478 (mmm) cc_final: 0.8202 (mmm) REVERT: D 82 LEU cc_start: 0.8714 (mt) cc_final: 0.8446 (tp) REVERT: D 91 TYR cc_start: 0.7503 (m-80) cc_final: 0.6921 (m-10) REVERT: D 102 TYR cc_start: 0.9404 (m-80) cc_final: 0.8932 (m-80) REVERT: E 37 GLN cc_start: 0.7924 (pp30) cc_final: 0.7326 (pp30) REVERT: E 45 LYS cc_start: 0.8696 (tptp) cc_final: 0.8078 (ttpp) REVERT: E 72 THR cc_start: 0.6932 (t) cc_final: 0.6447 (t) REVERT: F 573 ILE cc_start: 0.9254 (pt) cc_final: 0.9030 (pt) REVERT: F 577 GLN cc_start: 0.9149 (mt0) cc_final: 0.8821 (mt0) REVERT: F 584 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8797 (tm-30) REVERT: F 624 ASP cc_start: 0.8986 (m-30) cc_final: 0.8727 (m-30) REVERT: F 648 GLU cc_start: 0.9129 (pp20) cc_final: 0.8824 (pp20) REVERT: G 98 ASN cc_start: 0.8692 (t0) cc_final: 0.7537 (t0) REVERT: G 102 GLU cc_start: 0.9313 (mp0) cc_final: 0.8888 (mp0) REVERT: G 114 GLN cc_start: 0.9434 (tm-30) cc_final: 0.9132 (tm-30) REVERT: G 302 ASN cc_start: 0.8322 (t0) cc_final: 0.7750 (t0) REVERT: G 321 ASP cc_start: 0.8702 (t70) cc_final: 0.8285 (t70) REVERT: G 325 ASP cc_start: 0.8832 (p0) cc_final: 0.8245 (p0) REVERT: G 426 MET cc_start: 0.8801 (ptm) cc_final: 0.8309 (ptm) REVERT: G 434 MET cc_start: 0.8001 (tmm) cc_final: 0.7557 (tmm) REVERT: H 1 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8369 (pm20) REVERT: H 58 TYR cc_start: 0.5932 (p90) cc_final: 0.5675 (p90) REVERT: H 67 PHE cc_start: 0.8806 (p90) cc_final: 0.8253 (p90) REVERT: I 59 LYS cc_start: 0.8255 (tptp) cc_final: 0.8051 (tptp) REVERT: I 80 ASN cc_start: 0.9056 (t0) cc_final: 0.8621 (p0) REVERT: I 98 ASN cc_start: 0.8552 (t0) cc_final: 0.7752 (t0) REVERT: I 102 GLU cc_start: 0.9239 (mp0) cc_final: 0.8753 (mp0) REVERT: I 114 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9090 (tm-30) REVERT: I 211 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8794 (tm-30) REVERT: I 217 TYR cc_start: 0.7048 (m-10) cc_final: 0.6326 (m-10) REVERT: I 230 ASP cc_start: 0.8611 (t0) cc_final: 0.8393 (t0) REVERT: I 252 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8908 (mtpp) REVERT: I 328 MET cc_start: 0.8033 (ptp) cc_final: 0.7644 (ptp) REVERT: I 340 GLU cc_start: 0.9252 (tp30) cc_final: 0.9040 (tp30) REVERT: I 425 ASN cc_start: 0.9382 (p0) cc_final: 0.9119 (p0) REVERT: I 475 MET cc_start: 0.6439 (tmm) cc_final: 0.6141 (tmm) REVERT: I 482 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8597 (mm-30) REVERT: J 1 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8354 (pm20) REVERT: J 29 PHE cc_start: 0.8671 (t80) cc_final: 0.8409 (t80) REVERT: J 36 TRP cc_start: 0.8329 (m100) cc_final: 0.7833 (m100) REVERT: J 44 ARG cc_start: 0.5710 (mmt-90) cc_final: 0.5220 (mmt-90) REVERT: J 82 LEU cc_start: 0.8541 (mt) cc_final: 0.8069 (tp) REVERT: J 85 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8107 (tm-30) REVERT: J 91 TYR cc_start: 0.8661 (m-80) cc_final: 0.8179 (m-80) REVERT: J 102 TYR cc_start: 0.9316 (m-80) cc_final: 0.8569 (m-80) REVERT: K 23 CYS cc_start: 0.8910 (t) cc_final: 0.8235 (t) REVERT: K 37 GLN cc_start: 0.8065 (pp30) cc_final: 0.7148 (pp30) REVERT: K 38 GLN cc_start: 0.8660 (pt0) cc_final: 0.7579 (tt0) REVERT: K 45 LYS cc_start: 0.9016 (tptm) cc_final: 0.8800 (ttpt) REVERT: L 37 GLN cc_start: 0.8081 (pp30) cc_final: 0.7269 (pp30) REVERT: L 38 GLN cc_start: 0.8658 (pt0) cc_final: 0.7573 (tt0) REVERT: L 97 THR cc_start: 0.9055 (m) cc_final: 0.8832 (p) outliers start: 9 outliers final: 5 residues processed: 604 average time/residue: 0.3133 time to fit residues: 290.9995 Evaluate side-chains 454 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 449 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 258 GLN B 276 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 440 GLN I 66 HIS I 137 ASN ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068661 restraints weight = 65246.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070941 restraints weight = 35021.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.072492 restraints weight = 22880.791| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20587 Z= 0.299 Angle : 0.873 17.020 27934 Z= 0.423 Chirality : 0.052 0.364 3337 Planarity : 0.005 0.084 3463 Dihedral : 11.687 96.097 4330 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 16.12 % Favored : 83.67 % Rotamer: Outliers : 0.09 % Allowed : 6.63 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -4.03 (0.15), residues: 2388 helix: -1.71 (0.25), residues: 357 sheet: -1.29 (0.27), residues: 393 loop : -3.54 (0.12), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 479 HIS 0.009 0.002 HIS K 76 PHE 0.025 0.002 PHE D 27 TYR 0.030 0.002 TYR I 217 ARG 0.006 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 549 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 MET cc_start: 0.8915 (mmt) cc_final: 0.8675 (mmm) REVERT: A 584 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 617 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8042 (mtm-85) REVERT: A 622 ILE cc_start: 0.9149 (pt) cc_final: 0.8843 (mp) REVERT: A 626 MET cc_start: 0.8266 (mtm) cc_final: 0.7712 (mtm) REVERT: A 635 ILE cc_start: 0.9402 (mp) cc_final: 0.9020 (mp) REVERT: A 648 GLU cc_start: 0.9166 (pp20) cc_final: 0.8875 (pp20) REVERT: B 98 ASN cc_start: 0.8255 (t0) cc_final: 0.7620 (t0) REVERT: B 114 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9128 (tm-30) REVERT: B 161 MET cc_start: 0.9234 (tpp) cc_final: 0.8995 (tpp) REVERT: B 321 ASP cc_start: 0.9073 (t70) cc_final: 0.8715 (t70) REVERT: B 452 LEU cc_start: 0.9462 (pt) cc_final: 0.8894 (pp) REVERT: C 530 MET cc_start: 0.8808 (mmp) cc_final: 0.8347 (mmp) REVERT: C 584 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 617 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8123 (mtm180) REVERT: C 621 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 626 MET cc_start: 0.8186 (mtm) cc_final: 0.7610 (mtm) REVERT: C 648 GLU cc_start: 0.9162 (pp20) cc_final: 0.8725 (pm20) REVERT: D 34 MET cc_start: 0.9262 (mpp) cc_final: 0.9042 (mmm) REVERT: D 39 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8608 (mm110) REVERT: D 44 ARG cc_start: 0.6975 (mmt180) cc_final: 0.6705 (mmt-90) REVERT: D 91 TYR cc_start: 0.7868 (m-80) cc_final: 0.7156 (m-10) REVERT: D 102 TYR cc_start: 0.9410 (m-80) cc_final: 0.9039 (m-80) REVERT: E 37 GLN cc_start: 0.7892 (pp30) cc_final: 0.7370 (pp30) REVERT: E 38 GLN cc_start: 0.8662 (pt0) cc_final: 0.8457 (pt0) REVERT: E 45 LYS cc_start: 0.8880 (tptp) cc_final: 0.8448 (ttpp) REVERT: E 72 THR cc_start: 0.7214 (t) cc_final: 0.6567 (t) REVERT: E 82 ASP cc_start: 0.8915 (m-30) cc_final: 0.8705 (m-30) REVERT: E 97 THR cc_start: 0.9061 (m) cc_final: 0.8770 (p) REVERT: F 536 THR cc_start: 0.9240 (m) cc_final: 0.8887 (p) REVERT: F 573 ILE cc_start: 0.9225 (pt) cc_final: 0.8989 (pt) REVERT: F 577 GLN cc_start: 0.9205 (mt0) cc_final: 0.8789 (mt0) REVERT: F 584 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8663 (tm-30) REVERT: F 621 GLU cc_start: 0.8696 (tm-30) cc_final: 0.7351 (tm-30) REVERT: F 626 MET cc_start: 0.7562 (mtt) cc_final: 0.7129 (mpp) REVERT: F 648 GLU cc_start: 0.9059 (pp20) cc_final: 0.8577 (pm20) REVERT: F 658 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8567 (tm-30) REVERT: G 114 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9176 (tm-30) REVERT: G 150 MET cc_start: 0.9067 (tmm) cc_final: 0.8801 (tmm) REVERT: G 161 MET cc_start: 0.9197 (tpp) cc_final: 0.8983 (tpp) REVERT: G 252 LYS cc_start: 0.9481 (mmtp) cc_final: 0.9140 (mmmm) REVERT: G 302 ASN cc_start: 0.8534 (t0) cc_final: 0.8174 (t0) REVERT: G 321 ASP cc_start: 0.8778 (t70) cc_final: 0.8434 (t70) REVERT: G 325 ASP cc_start: 0.8958 (p0) cc_final: 0.8401 (p0) REVERT: G 426 MET cc_start: 0.8628 (ptm) cc_final: 0.8253 (ptm) REVERT: G 434 MET cc_start: 0.8233 (tmm) cc_final: 0.7783 (tmm) REVERT: H 1 GLU cc_start: 0.8967 (tm-30) cc_final: 0.7983 (pm20) REVERT: H 27 PHE cc_start: 0.8360 (m-10) cc_final: 0.7875 (m-80) REVERT: H 44 ARG cc_start: 0.5839 (mmt180) cc_final: 0.5398 (mmt-90) REVERT: H 67 PHE cc_start: 0.8882 (p90) cc_final: 0.8149 (p90) REVERT: H 91 TYR cc_start: 0.8476 (m-10) cc_final: 0.8267 (m-10) REVERT: I 59 LYS cc_start: 0.8061 (tptp) cc_final: 0.7843 (tptp) REVERT: I 98 ASN cc_start: 0.8515 (t0) cc_final: 0.7929 (t0) REVERT: I 102 GLU cc_start: 0.9322 (mp0) cc_final: 0.8766 (mp0) REVERT: I 104 MET cc_start: 0.9310 (mmt) cc_final: 0.8824 (mmt) REVERT: I 114 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9149 (tm-30) REVERT: I 205 CYS cc_start: 0.7261 (t) cc_final: 0.7060 (t) REVERT: I 217 TYR cc_start: 0.7013 (m-10) cc_final: 0.6787 (m-10) REVERT: I 252 LYS cc_start: 0.9353 (mtmm) cc_final: 0.8982 (mtpp) REVERT: I 321 ASP cc_start: 0.8729 (t70) cc_final: 0.8466 (t70) REVERT: I 425 ASN cc_start: 0.9346 (p0) cc_final: 0.9051 (p0) REVERT: I 482 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8681 (mm-30) REVERT: J 1 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8352 (pm20) REVERT: J 36 TRP cc_start: 0.8326 (m100) cc_final: 0.7997 (m100) REVERT: J 47 TRP cc_start: 0.5888 (m-90) cc_final: 0.5686 (m-90) REVERT: J 58 TYR cc_start: 0.5898 (p90) cc_final: 0.5558 (p90) REVERT: J 64 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8705 (mmmt) REVERT: J 82 LEU cc_start: 0.8870 (mt) cc_final: 0.8343 (tp) REVERT: J 85 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8125 (tm-30) REVERT: K 27 TYR cc_start: 0.7704 (p90) cc_final: 0.7423 (p90) REVERT: K 37 GLN cc_start: 0.8086 (pp30) cc_final: 0.7486 (pp30) REVERT: K 45 LYS cc_start: 0.9057 (tptm) cc_final: 0.8736 (ttpp) REVERT: K 81 GLU cc_start: 0.9223 (pp20) cc_final: 0.8871 (pp20) REVERT: L 37 GLN cc_start: 0.7939 (pp30) cc_final: 0.7320 (pp30) REVERT: L 38 GLN cc_start: 0.8556 (pt0) cc_final: 0.7624 (tt0) REVERT: L 82 ASP cc_start: 0.8954 (m-30) cc_final: 0.7698 (m-30) outliers start: 2 outliers final: 1 residues processed: 550 average time/residue: 0.3182 time to fit residues: 267.4790 Evaluate side-chains 423 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 422 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS B 66 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 585 HIS F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070377 restraints weight = 69251.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072635 restraints weight = 37635.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074171 restraints weight = 24944.591| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20587 Z= 0.228 Angle : 0.840 16.055 27934 Z= 0.409 Chirality : 0.052 0.327 3337 Planarity : 0.005 0.084 3463 Dihedral : 10.671 94.286 4330 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.32 % Favored : 85.51 % Rotamer: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % 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: -3.84 (0.15), residues: 2388 helix: -1.54 (0.25), residues: 369 sheet: -1.11 (0.27), residues: 405 loop : -3.45 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 479 HIS 0.011 0.002 HIS L 76 PHE 0.016 0.001 PHE L 98 TYR 0.034 0.002 TYR H 90 ARG 0.006 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 545 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8639 (tm-30) REVERT: A 617 ARG cc_start: 0.8734 (mtt180) cc_final: 0.8383 (mtm-85) REVERT: A 626 MET cc_start: 0.8339 (mtm) cc_final: 0.7987 (mtm) REVERT: A 648 GLU cc_start: 0.9161 (pp20) cc_final: 0.8844 (pp20) REVERT: B 98 ASN cc_start: 0.8136 (t0) cc_final: 0.6852 (t0) REVERT: B 102 GLU cc_start: 0.9346 (mp0) cc_final: 0.9033 (mp0) REVERT: B 104 MET cc_start: 0.9319 (ttp) cc_final: 0.9018 (ttp) REVERT: B 114 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9141 (tm-30) REVERT: B 161 MET cc_start: 0.9229 (tpp) cc_final: 0.8987 (tpp) REVERT: B 452 LEU cc_start: 0.9433 (pt) cc_final: 0.9117 (pp) REVERT: C 584 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 617 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8206 (mtm180) REVERT: C 621 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 626 MET cc_start: 0.8020 (mtm) cc_final: 0.7772 (mtm) REVERT: C 648 GLU cc_start: 0.9141 (pp20) cc_final: 0.8702 (pm20) REVERT: D 39 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8452 (tm-30) REVERT: D 44 ARG cc_start: 0.6540 (mmt180) cc_final: 0.6048 (mmt-90) REVERT: D 67 PHE cc_start: 0.8644 (p90) cc_final: 0.8391 (p90) REVERT: D 87 THR cc_start: 0.8007 (p) cc_final: 0.7414 (p) REVERT: E 37 GLN cc_start: 0.7836 (pp30) cc_final: 0.7226 (pp30) REVERT: E 38 GLN cc_start: 0.8667 (pt0) cc_final: 0.8424 (pt0) REVERT: E 45 LYS cc_start: 0.8860 (tptp) cc_final: 0.8447 (ttpp) REVERT: E 82 ASP cc_start: 0.8969 (m-30) cc_final: 0.8654 (m-30) REVERT: F 535 MET cc_start: 0.8722 (mmt) cc_final: 0.8325 (mmm) REVERT: F 573 ILE cc_start: 0.9158 (pt) cc_final: 0.8888 (pt) REVERT: F 577 GLN cc_start: 0.9208 (mt0) cc_final: 0.8780 (mt0) REVERT: F 584 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8610 (tm-30) REVERT: F 621 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8546 (tm-30) REVERT: F 648 GLU cc_start: 0.9107 (pp20) cc_final: 0.8630 (pm20) REVERT: F 658 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8607 (tm-30) REVERT: G 92 GLU cc_start: 0.5369 (pt0) cc_final: 0.5108 (pt0) REVERT: G 98 ASN cc_start: 0.8261 (t0) cc_final: 0.7877 (t0) REVERT: G 104 MET cc_start: 0.9259 (ttp) cc_final: 0.8986 (ttp) REVERT: G 114 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9182 (tm-30) REVERT: G 150 MET cc_start: 0.9048 (tmm) cc_final: 0.8800 (tmm) REVERT: G 252 LYS cc_start: 0.9475 (mmtp) cc_final: 0.9133 (mmmm) REVERT: G 302 ASN cc_start: 0.8348 (t0) cc_final: 0.8092 (t0) REVERT: G 321 ASP cc_start: 0.8892 (t70) cc_final: 0.8599 (t70) REVERT: G 325 ASP cc_start: 0.9032 (p0) cc_final: 0.8469 (p0) REVERT: G 426 MET cc_start: 0.8499 (ptm) cc_final: 0.8189 (ptm) REVERT: G 434 MET cc_start: 0.8217 (tmm) cc_final: 0.7789 (tmm) REVERT: H 1 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8599 (tm-30) REVERT: H 67 PHE cc_start: 0.8427 (p90) cc_final: 0.8037 (p90) REVERT: I 59 LYS cc_start: 0.8057 (tptp) cc_final: 0.7825 (tptp) REVERT: I 98 ASN cc_start: 0.8400 (t0) cc_final: 0.7872 (t0) REVERT: I 102 GLU cc_start: 0.9314 (mp0) cc_final: 0.8646 (mp0) REVERT: I 104 MET cc_start: 0.9501 (mmt) cc_final: 0.8930 (tpp) REVERT: I 114 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9125 (tm-30) REVERT: I 230 ASP cc_start: 0.8784 (t0) cc_final: 0.8492 (t0) REVERT: I 252 LYS cc_start: 0.9347 (mtmm) cc_final: 0.8985 (mtpp) REVERT: I 425 ASN cc_start: 0.9314 (p0) cc_final: 0.9029 (p0) REVERT: I 434 MET cc_start: 0.9293 (tpp) cc_final: 0.8761 (tpp) REVERT: I 482 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8726 (mm-30) REVERT: J 1 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8297 (pm20) REVERT: J 36 TRP cc_start: 0.8528 (m100) cc_final: 0.8060 (m100) REVERT: J 57 THR cc_start: 0.7821 (m) cc_final: 0.7336 (m) REVERT: J 67 PHE cc_start: 0.8692 (p90) cc_final: 0.8085 (p90) REVERT: K 27 TYR cc_start: 0.7679 (p90) cc_final: 0.7225 (p90) REVERT: K 37 GLN cc_start: 0.8182 (pp30) cc_final: 0.7651 (pp30) REVERT: K 45 LYS cc_start: 0.9151 (tptm) cc_final: 0.8760 (ttpt) REVERT: K 82 ASP cc_start: 0.9104 (m-30) cc_final: 0.8693 (m-30) REVERT: L 37 GLN cc_start: 0.8014 (pp30) cc_final: 0.7377 (pp30) REVERT: L 38 GLN cc_start: 0.8866 (pt0) cc_final: 0.8422 (pt0) outliers start: 2 outliers final: 0 residues processed: 546 average time/residue: 0.3093 time to fit residues: 259.1454 Evaluate side-chains 416 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 237 optimal weight: 0.0170 chunk 236 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 66 optimal weight: 0.0040 chunk 78 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN I 66 HIS I 137 ASN ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069871 restraints weight = 69273.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.072112 restraints weight = 37690.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073632 restraints weight = 24990.134| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20587 Z= 0.241 Angle : 0.837 15.378 27934 Z= 0.407 Chirality : 0.052 0.350 3337 Planarity : 0.005 0.082 3463 Dihedral : 10.289 92.845 4330 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.54 % Favored : 84.30 % Rotamer: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % 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: -3.75 (0.15), residues: 2388 helix: -1.31 (0.26), residues: 357 sheet: -1.17 (0.27), residues: 390 loop : -3.37 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 35 HIS 0.009 0.002 HIS E 76 PHE 0.020 0.002 PHE J 29 TYR 0.019 0.002 TYR L 32 ARG 0.006 0.001 ARG J 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8600 (tm-30) REVERT: A 617 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8323 (mtm-85) REVERT: A 626 MET cc_start: 0.8304 (mtm) cc_final: 0.7870 (mtm) REVERT: A 635 ILE cc_start: 0.9395 (mp) cc_final: 0.8727 (mp) REVERT: A 648 GLU cc_start: 0.9186 (pp20) cc_final: 0.8847 (pp20) REVERT: A 654 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8840 (tp30) REVERT: B 98 ASN cc_start: 0.7924 (t0) cc_final: 0.7574 (t0) REVERT: B 114 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9163 (tm-30) REVERT: B 121 LYS cc_start: 0.9287 (ttmt) cc_final: 0.9028 (ttpp) REVERT: B 161 MET cc_start: 0.9208 (tpp) cc_final: 0.8967 (tpp) REVERT: B 427 TRP cc_start: 0.8711 (m100) cc_final: 0.8351 (m100) REVERT: B 479 TRP cc_start: 0.9267 (m-90) cc_final: 0.8938 (m-90) REVERT: C 584 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 588 ARG cc_start: 0.9224 (ttt180) cc_final: 0.8902 (ttm-80) REVERT: C 617 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8240 (mtm180) REVERT: C 621 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 622 ILE cc_start: 0.9253 (pt) cc_final: 0.8886 (pt) REVERT: C 626 MET cc_start: 0.8015 (mtm) cc_final: 0.7456 (mtm) REVERT: C 648 GLU cc_start: 0.9173 (pp20) cc_final: 0.8739 (pm20) REVERT: D 39 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8528 (tm-30) REVERT: D 67 PHE cc_start: 0.8774 (p90) cc_final: 0.8363 (p90) REVERT: D 87 THR cc_start: 0.8013 (p) cc_final: 0.7346 (p) REVERT: D 91 TYR cc_start: 0.8394 (m-80) cc_final: 0.8181 (m-10) REVERT: E 38 GLN cc_start: 0.8664 (pt0) cc_final: 0.8430 (pt0) REVERT: E 45 LYS cc_start: 0.8837 (tptp) cc_final: 0.8480 (ttpp) REVERT: E 82 ASP cc_start: 0.9010 (m-30) cc_final: 0.8646 (m-30) REVERT: F 535 MET cc_start: 0.8852 (mmt) cc_final: 0.8556 (mmm) REVERT: F 573 ILE cc_start: 0.9155 (pt) cc_final: 0.8887 (pt) REVERT: F 577 GLN cc_start: 0.9153 (mt0) cc_final: 0.8735 (mt0) REVERT: F 584 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 621 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8523 (tm-30) REVERT: F 648 GLU cc_start: 0.9159 (pp20) cc_final: 0.8654 (pm20) REVERT: F 658 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8589 (tm-30) REVERT: G 104 MET cc_start: 0.9295 (ttp) cc_final: 0.9091 (mtp) REVERT: G 114 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9195 (tm-30) REVERT: G 150 MET cc_start: 0.9068 (tmm) cc_final: 0.8571 (tmm) REVERT: G 161 MET cc_start: 0.9153 (tpp) cc_final: 0.8943 (tpp) REVERT: G 252 LYS cc_start: 0.9458 (mmtp) cc_final: 0.9125 (mmmm) REVERT: G 434 MET cc_start: 0.8287 (tmm) cc_final: 0.7873 (tmm) REVERT: H 44 ARG cc_start: 0.6118 (mmt180) cc_final: 0.5718 (mmt-90) REVERT: H 67 PHE cc_start: 0.8680 (p90) cc_final: 0.8023 (p90) REVERT: H 72 ASP cc_start: 0.8937 (t70) cc_final: 0.8658 (t0) REVERT: I 59 LYS cc_start: 0.8049 (tptp) cc_final: 0.7816 (tptp) REVERT: I 98 ASN cc_start: 0.8323 (t0) cc_final: 0.7743 (t0) REVERT: I 102 GLU cc_start: 0.9310 (mp0) cc_final: 0.8702 (mp0) REVERT: I 104 MET cc_start: 0.9589 (mmt) cc_final: 0.9313 (mmm) REVERT: I 114 GLN cc_start: 0.9450 (tm-30) cc_final: 0.9123 (tm-30) REVERT: I 180 ASP cc_start: 0.8871 (m-30) cc_final: 0.8662 (m-30) REVERT: I 205 CYS cc_start: 0.7449 (t) cc_final: 0.7207 (t) REVERT: I 230 ASP cc_start: 0.8625 (t0) cc_final: 0.8352 (t0) REVERT: I 252 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8954 (mtpp) REVERT: I 425 ASN cc_start: 0.9331 (p0) cc_final: 0.9060 (p0) REVERT: I 434 MET cc_start: 0.9238 (tpp) cc_final: 0.8760 (tpp) REVERT: J 1 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8307 (pm20) REVERT: J 36 TRP cc_start: 0.8500 (m100) cc_final: 0.7925 (m100) REVERT: J 57 THR cc_start: 0.7722 (m) cc_final: 0.6915 (m) REVERT: J 67 PHE cc_start: 0.8772 (p90) cc_final: 0.7960 (p90) REVERT: K 27 TYR cc_start: 0.7577 (p90) cc_final: 0.7331 (p90) REVERT: K 37 GLN cc_start: 0.8123 (pp30) cc_final: 0.7445 (pp30) REVERT: K 45 LYS cc_start: 0.9175 (tptm) cc_final: 0.8777 (ttpp) REVERT: K 82 ASP cc_start: 0.8874 (m-30) cc_final: 0.7850 (m-30) REVERT: L 37 GLN cc_start: 0.8023 (pp30) cc_final: 0.7220 (pp30) REVERT: L 38 GLN cc_start: 0.8830 (pt0) cc_final: 0.8462 (pt0) outliers start: 2 outliers final: 1 residues processed: 533 average time/residue: 0.3130 time to fit residues: 256.1644 Evaluate side-chains 415 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 203 GLN B 330 HIS B 352 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN G 66 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 GLN G 330 HIS G 440 GLN ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.065099 restraints weight = 71337.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.067169 restraints weight = 39427.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.068588 restraints weight = 26598.805| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20587 Z= 0.469 Angle : 0.988 14.514 27934 Z= 0.480 Chirality : 0.056 0.366 3337 Planarity : 0.006 0.075 3463 Dihedral : 10.748 96.998 4330 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.01 % Favored : 81.87 % Rotamer: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % 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: -4.00 (0.15), residues: 2388 helix: -1.28 (0.25), residues: 366 sheet: -1.31 (0.26), residues: 405 loop : -3.64 (0.12), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 35 HIS 0.010 0.002 HIS L 76 PHE 0.022 0.002 PHE J 29 TYR 0.026 0.003 TYR K 32 ARG 0.005 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 648 GLU cc_start: 0.9221 (pp20) cc_final: 0.8759 (pm20) REVERT: A 654 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8579 (tp30) REVERT: B 98 ASN cc_start: 0.8352 (t0) cc_final: 0.7717 (t0) REVERT: B 121 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9115 (ttpp) REVERT: B 203 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: C 530 MET cc_start: 0.9074 (mmp) cc_final: 0.8819 (mmp) REVERT: C 584 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 621 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 622 ILE cc_start: 0.9337 (pt) cc_final: 0.8972 (pt) REVERT: C 626 MET cc_start: 0.8143 (mtm) cc_final: 0.7727 (mtm) REVERT: C 648 GLU cc_start: 0.9264 (pp20) cc_final: 0.8709 (pm20) REVERT: D 67 PHE cc_start: 0.8732 (p90) cc_final: 0.8395 (p90) REVERT: D 91 TYR cc_start: 0.8704 (m-80) cc_final: 0.7883 (m-80) REVERT: D 102 TYR cc_start: 0.9394 (m-80) cc_final: 0.9160 (m-80) REVERT: E 33 MET cc_start: 0.7858 (ptt) cc_final: 0.6524 (mtm) REVERT: E 37 GLN cc_start: 0.7495 (pp30) cc_final: 0.7253 (pp30) REVERT: E 38 GLN cc_start: 0.8482 (pt0) cc_final: 0.8187 (pt0) REVERT: E 45 LYS cc_start: 0.9031 (tptp) cc_final: 0.8663 (ttpp) REVERT: E 82 ASP cc_start: 0.9044 (m-30) cc_final: 0.8717 (m-30) REVERT: E 96 TYR cc_start: 0.8420 (m-10) cc_final: 0.8196 (m-10) REVERT: F 573 ILE cc_start: 0.9221 (pt) cc_final: 0.8940 (pt) REVERT: F 577 GLN cc_start: 0.9201 (mt0) cc_final: 0.8767 (mt0) REVERT: F 584 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8800 (tm-30) REVERT: F 621 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8611 (tm-30) REVERT: F 624 ASP cc_start: 0.8785 (m-30) cc_final: 0.8550 (m-30) REVERT: F 648 GLU cc_start: 0.9249 (pp20) cc_final: 0.8717 (pm20) REVERT: F 658 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8719 (tm-30) REVERT: G 114 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9209 (tm-30) REVERT: G 150 MET cc_start: 0.9112 (tmm) cc_final: 0.8844 (tmm) REVERT: G 434 MET cc_start: 0.8255 (tmm) cc_final: 0.7914 (tmm) REVERT: G 475 MET cc_start: 0.8082 (tmm) cc_final: 0.7383 (tmm) REVERT: H 1 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8049 (pm20) REVERT: H 58 TYR cc_start: 0.6025 (p90) cc_final: 0.5797 (p90) REVERT: H 67 PHE cc_start: 0.8616 (p90) cc_final: 0.7865 (p90) REVERT: I 59 LYS cc_start: 0.8160 (tptp) cc_final: 0.7901 (tptp) REVERT: I 104 MET cc_start: 0.9540 (mmt) cc_final: 0.9244 (mmm) REVERT: I 114 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9106 (tm-30) REVERT: I 252 LYS cc_start: 0.9387 (mtmm) cc_final: 0.9120 (mmmm) REVERT: I 425 ASN cc_start: 0.9349 (p0) cc_final: 0.9077 (p0) REVERT: J 36 TRP cc_start: 0.8620 (m100) cc_final: 0.8017 (m100) REVERT: J 57 THR cc_start: 0.7863 (m) cc_final: 0.7106 (m) REVERT: J 67 PHE cc_start: 0.8658 (p90) cc_final: 0.8023 (p90) REVERT: J 102 TYR cc_start: 0.9186 (m-80) cc_final: 0.8841 (m-80) REVERT: K 35 TRP cc_start: 0.8692 (m-10) cc_final: 0.8318 (m-10) REVERT: K 45 LYS cc_start: 0.9123 (tptm) cc_final: 0.8760 (ttpt) REVERT: L 37 GLN cc_start: 0.8042 (pp30) cc_final: 0.7475 (pp30) REVERT: L 38 GLN cc_start: 0.8664 (pt0) cc_final: 0.8191 (pt0) outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.3108 time to fit residues: 223.7026 Evaluate side-chains 382 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.067852 restraints weight = 69149.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.070030 restraints weight = 37776.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071531 restraints weight = 25241.274| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20587 Z= 0.248 Angle : 0.867 13.899 27934 Z= 0.424 Chirality : 0.053 0.331 3337 Planarity : 0.005 0.071 3463 Dihedral : 10.160 91.978 4330 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.45 % Favored : 84.42 % Rotamer: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.84 (0.15), residues: 2388 helix: -1.08 (0.26), residues: 366 sheet: -1.32 (0.26), residues: 390 loop : -3.50 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 479 HIS 0.010 0.002 HIS L 76 PHE 0.020 0.001 PHE J 29 TYR 0.027 0.002 TYR J 58 ARG 0.004 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 505 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 617 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8106 (mtm-85) REVERT: A 626 MET cc_start: 0.8073 (mtm) cc_final: 0.7724 (mtm) REVERT: A 648 GLU cc_start: 0.9229 (pp20) cc_final: 0.8749 (pm20) REVERT: A 654 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8449 (tp30) REVERT: A 657 GLU cc_start: 0.8960 (mp0) cc_final: 0.8310 (mp0) REVERT: B 98 ASN cc_start: 0.7944 (t0) cc_final: 0.7363 (t0) REVERT: B 195 ASN cc_start: 0.8224 (p0) cc_final: 0.7894 (m-40) REVERT: B 427 TRP cc_start: 0.8839 (m100) cc_final: 0.8517 (m100) REVERT: B 479 TRP cc_start: 0.9311 (m-90) cc_final: 0.8927 (m-90) REVERT: C 584 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 617 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8200 (mtm180) REVERT: C 621 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 622 ILE cc_start: 0.9283 (pt) cc_final: 0.8845 (pt) REVERT: C 626 MET cc_start: 0.8115 (mtm) cc_final: 0.7114 (mtm) REVERT: C 648 GLU cc_start: 0.9227 (pp20) cc_final: 0.8681 (pm20) REVERT: C 657 GLU cc_start: 0.9187 (mp0) cc_final: 0.8587 (mp0) REVERT: D 57 THR cc_start: 0.7849 (m) cc_final: 0.7545 (m) REVERT: D 67 PHE cc_start: 0.8684 (p90) cc_final: 0.7938 (p90) REVERT: D 91 TYR cc_start: 0.8499 (m-80) cc_final: 0.8047 (m-10) REVERT: E 33 MET cc_start: 0.7872 (ptt) cc_final: 0.6935 (mtm) REVERT: E 38 GLN cc_start: 0.8409 (pt0) cc_final: 0.8086 (pt0) REVERT: E 45 LYS cc_start: 0.9014 (tptp) cc_final: 0.8590 (ttpp) REVERT: E 82 ASP cc_start: 0.9042 (m-30) cc_final: 0.8736 (m-30) REVERT: F 573 ILE cc_start: 0.9190 (pt) cc_final: 0.8888 (pt) REVERT: F 577 GLN cc_start: 0.9168 (mt0) cc_final: 0.8709 (mt0) REVERT: F 584 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8768 (tm-30) REVERT: F 621 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8534 (tm-30) REVERT: F 624 ASP cc_start: 0.8858 (m-30) cc_final: 0.8650 (m-30) REVERT: F 648 GLU cc_start: 0.9198 (pp20) cc_final: 0.8643 (pm20) REVERT: F 658 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8686 (tm-30) REVERT: G 98 ASN cc_start: 0.8573 (t0) cc_final: 0.8368 (t0) REVERT: G 104 MET cc_start: 0.9209 (ttp) cc_final: 0.8681 (ttp) REVERT: G 114 GLN cc_start: 0.9483 (tm-30) cc_final: 0.9198 (tm-30) REVERT: G 150 MET cc_start: 0.9090 (tmm) cc_final: 0.8816 (tmm) REVERT: G 302 ASN cc_start: 0.8422 (t0) cc_final: 0.8198 (t0) REVERT: G 427 TRP cc_start: 0.8665 (m-90) cc_final: 0.8169 (m-90) REVERT: G 434 MET cc_start: 0.8201 (tmm) cc_final: 0.7909 (tmm) REVERT: H 1 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8018 (pm20) REVERT: H 18 LEU cc_start: 0.7887 (mm) cc_final: 0.7686 (mm) REVERT: H 44 ARG cc_start: 0.6192 (mmt180) cc_final: 0.5950 (mmt-90) REVERT: H 47 TRP cc_start: 0.6584 (m-90) cc_final: 0.5951 (m-90) REVERT: H 58 TYR cc_start: 0.6050 (p90) cc_final: 0.5735 (p90) REVERT: H 72 ASP cc_start: 0.8937 (t70) cc_final: 0.8723 (t0) REVERT: H 85 GLU cc_start: 0.8784 (pp20) cc_final: 0.8427 (pp20) REVERT: I 59 LYS cc_start: 0.8080 (tptp) cc_final: 0.7835 (tptp) REVERT: I 98 ASN cc_start: 0.8332 (t0) cc_final: 0.7739 (t0) REVERT: I 102 GLU cc_start: 0.9356 (mp0) cc_final: 0.8831 (mp0) REVERT: I 104 MET cc_start: 0.9436 (mmt) cc_final: 0.8665 (mmm) REVERT: I 114 GLN cc_start: 0.9507 (tm-30) cc_final: 0.9170 (tm-30) REVERT: I 252 LYS cc_start: 0.9349 (mtmm) cc_final: 0.9085 (mmmm) REVERT: I 425 ASN cc_start: 0.9326 (p0) cc_final: 0.9060 (p0) REVERT: J 36 TRP cc_start: 0.8486 (m100) cc_final: 0.7993 (m100) REVERT: J 57 THR cc_start: 0.7821 (m) cc_final: 0.7044 (m) REVERT: J 67 PHE cc_start: 0.8615 (p90) cc_final: 0.7993 (p90) REVERT: K 37 GLN cc_start: 0.7526 (pp30) cc_final: 0.6960 (pp30) REVERT: K 45 LYS cc_start: 0.9132 (tptm) cc_final: 0.8785 (ttpp) REVERT: L 37 GLN cc_start: 0.7998 (pp30) cc_final: 0.7190 (pp30) REVERT: L 38 GLN cc_start: 0.8656 (pt0) cc_final: 0.8053 (pt0) outliers start: 2 outliers final: 0 residues processed: 506 average time/residue: 0.3161 time to fit residues: 246.5878 Evaluate side-chains 401 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 585 HIS F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.069029 restraints weight = 69112.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.071247 restraints weight = 37675.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072757 restraints weight = 25061.432| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20587 Z= 0.219 Angle : 0.845 14.398 27934 Z= 0.412 Chirality : 0.054 0.729 3337 Planarity : 0.005 0.068 3463 Dihedral : 9.911 88.957 4330 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.37 % Favored : 83.54 % Rotamer: Outliers : 0.14 % Allowed : 1.61 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.39 % 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: -3.74 (0.15), residues: 2388 helix: -0.96 (0.26), residues: 366 sheet: -1.28 (0.26), residues: 390 loop : -3.43 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 35 HIS 0.010 0.002 HIS L 76 PHE 0.016 0.001 PHE J 29 TYR 0.032 0.002 TYR J 58 ARG 0.004 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 617 ARG cc_start: 0.8473 (mtt180) cc_final: 0.7977 (mtm-85) REVERT: A 626 MET cc_start: 0.8063 (mtm) cc_final: 0.7811 (mtt) REVERT: A 648 GLU cc_start: 0.9208 (pp20) cc_final: 0.8746 (pm20) REVERT: A 658 GLN cc_start: 0.9359 (tt0) cc_final: 0.8806 (tm-30) REVERT: B 121 LYS cc_start: 0.9294 (ttmt) cc_final: 0.9062 (ttpp) REVERT: B 150 MET cc_start: 0.9255 (tmm) cc_final: 0.9035 (tmm) REVERT: B 195 ASN cc_start: 0.8451 (p0) cc_final: 0.8089 (m-40) REVERT: B 479 TRP cc_start: 0.9298 (m-90) cc_final: 0.8946 (m-90) REVERT: C 584 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 617 ARG cc_start: 0.8545 (mtt180) cc_final: 0.8288 (mtm-85) REVERT: C 621 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 622 ILE cc_start: 0.9278 (pt) cc_final: 0.8646 (pt) REVERT: C 626 MET cc_start: 0.8175 (mtm) cc_final: 0.7326 (mtm) REVERT: C 645 LEU cc_start: 0.9381 (tp) cc_final: 0.8942 (tp) REVERT: C 648 GLU cc_start: 0.9196 (pp20) cc_final: 0.8678 (pm20) REVERT: C 657 GLU cc_start: 0.9227 (mp0) cc_final: 0.8583 (mp0) REVERT: D 36 TRP cc_start: 0.8564 (m100) cc_final: 0.8185 (m-10) REVERT: D 44 ARG cc_start: 0.5908 (mmt-90) cc_final: 0.4607 (mmt-90) REVERT: D 57 THR cc_start: 0.7831 (m) cc_final: 0.7562 (m) REVERT: D 67 PHE cc_start: 0.8755 (p90) cc_final: 0.7787 (p90) REVERT: D 71 ARG cc_start: 0.8475 (ttt-90) cc_final: 0.8186 (tmt-80) REVERT: D 89 MET cc_start: 0.8075 (mmp) cc_final: 0.6592 (tpt) REVERT: D 91 TYR cc_start: 0.8600 (m-80) cc_final: 0.8195 (m-10) REVERT: E 33 MET cc_start: 0.7704 (ptt) cc_final: 0.7376 (ptp) REVERT: E 37 GLN cc_start: 0.7709 (pp30) cc_final: 0.7415 (pp30) REVERT: E 38 GLN cc_start: 0.8454 (pt0) cc_final: 0.8074 (pt0) REVERT: E 45 LYS cc_start: 0.9032 (tptp) cc_final: 0.8786 (ttpp) REVERT: E 82 ASP cc_start: 0.9026 (m-30) cc_final: 0.8776 (m-30) REVERT: E 87 TYR cc_start: 0.8332 (m-80) cc_final: 0.7738 (m-80) REVERT: F 573 ILE cc_start: 0.9156 (pt) cc_final: 0.8845 (pt) REVERT: F 577 GLN cc_start: 0.9160 (mt0) cc_final: 0.8863 (mt0) REVERT: F 584 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8746 (tm-30) REVERT: F 621 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8507 (tm-30) REVERT: F 624 ASP cc_start: 0.8881 (m-30) cc_final: 0.8653 (m-30) REVERT: F 645 LEU cc_start: 0.9264 (tp) cc_final: 0.8779 (tp) REVERT: F 648 GLU cc_start: 0.9164 (pp20) cc_final: 0.8580 (pm20) REVERT: F 658 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8681 (tm-30) REVERT: G 98 ASN cc_start: 0.8571 (t0) cc_final: 0.7790 (t0) REVERT: G 102 GLU cc_start: 0.9314 (mp0) cc_final: 0.8889 (mp0) REVERT: G 104 MET cc_start: 0.9148 (ttp) cc_final: 0.8836 (ttp) REVERT: G 114 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9169 (tm-30) REVERT: G 150 MET cc_start: 0.9064 (tmm) cc_final: 0.8805 (tmm) REVERT: G 161 MET cc_start: 0.9203 (tpp) cc_final: 0.8995 (tpp) REVERT: G 302 ASN cc_start: 0.8488 (t0) cc_final: 0.8185 (t0) REVERT: G 426 MET cc_start: 0.8743 (ptm) cc_final: 0.8102 (ptm) REVERT: G 434 MET cc_start: 0.8221 (tmm) cc_final: 0.7882 (tmm) REVERT: H 1 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8124 (pm20) REVERT: H 47 TRP cc_start: 0.6626 (m-90) cc_final: 0.6306 (m-90) REVERT: H 67 PHE cc_start: 0.8797 (p90) cc_final: 0.8085 (p90) REVERT: H 72 ASP cc_start: 0.8917 (t70) cc_final: 0.8700 (t0) REVERT: I 59 LYS cc_start: 0.8031 (tptp) cc_final: 0.7786 (tptp) REVERT: I 98 ASN cc_start: 0.8216 (t0) cc_final: 0.7746 (t0) REVERT: I 102 GLU cc_start: 0.9379 (mp0) cc_final: 0.8973 (mp0) REVERT: I 114 GLN cc_start: 0.9480 (tm-30) cc_final: 0.9050 (tm-30) REVERT: I 217 TYR cc_start: 0.7677 (m-80) cc_final: 0.7138 (m-10) REVERT: I 252 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9036 (mmmm) REVERT: I 425 ASN cc_start: 0.9358 (p0) cc_final: 0.9144 (p0) REVERT: J 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7876 (m100) REVERT: J 44 ARG cc_start: 0.6055 (mmt180) cc_final: 0.4592 (mmt-90) REVERT: J 57 THR cc_start: 0.7756 (m) cc_final: 0.6885 (m) REVERT: J 67 PHE cc_start: 0.8588 (p90) cc_final: 0.7919 (p90) REVERT: K 37 GLN cc_start: 0.7254 (pp30) cc_final: 0.6920 (pp30) REVERT: K 45 LYS cc_start: 0.9183 (tptm) cc_final: 0.8851 (ttpp) REVERT: K 72 THR cc_start: 0.8569 (p) cc_final: 0.8229 (p) REVERT: K 87 TYR cc_start: 0.8390 (m-80) cc_final: 0.7826 (m-80) REVERT: K 103 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8147 (mtmm) REVERT: L 37 GLN cc_start: 0.8166 (pp30) cc_final: 0.7411 (pp30) REVERT: L 38 GLN cc_start: 0.8672 (pt0) cc_final: 0.8109 (pt0) REVERT: L 103 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8471 (mmmm) outliers start: 3 outliers final: 0 residues processed: 515 average time/residue: 0.3033 time to fit residues: 242.6755 Evaluate side-chains 409 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN F 585 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068059 restraints weight = 69624.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.070224 restraints weight = 38115.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.071714 restraints weight = 25552.261| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20587 Z= 0.279 Angle : 0.866 14.151 27934 Z= 0.425 Chirality : 0.055 0.770 3337 Planarity : 0.005 0.064 3463 Dihedral : 9.992 88.477 4330 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.91 % Favored : 83.96 % Rotamer: Outliers : 0.19 % Allowed : 0.85 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.39 % 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: -3.71 (0.15), residues: 2388 helix: -0.89 (0.26), residues: 369 sheet: -1.37 (0.27), residues: 375 loop : -3.38 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP K 35 HIS 0.009 0.002 HIS L 76 PHE 0.023 0.002 PHE J 29 TYR 0.042 0.002 TYR K 96 ARG 0.005 0.000 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 497 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 617 ARG cc_start: 0.8492 (mtt180) cc_final: 0.7926 (mtm-85) REVERT: A 648 GLU cc_start: 0.9191 (pp20) cc_final: 0.8863 (pp20) REVERT: A 657 GLU cc_start: 0.9072 (mp0) cc_final: 0.8411 (mp0) REVERT: A 658 GLN cc_start: 0.9255 (tt0) cc_final: 0.8858 (tm-30) REVERT: B 98 ASN cc_start: 0.8576 (t0) cc_final: 0.7444 (t0) REVERT: B 150 MET cc_start: 0.9256 (tmm) cc_final: 0.8984 (tmm) REVERT: B 195 ASN cc_start: 0.8130 (p0) cc_final: 0.7770 (m-40) REVERT: B 427 TRP cc_start: 0.8845 (m100) cc_final: 0.8487 (m100) REVERT: B 479 TRP cc_start: 0.9326 (m-90) cc_final: 0.8962 (m-90) REVERT: C 584 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 621 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 622 ILE cc_start: 0.9326 (pt) cc_final: 0.8958 (pt) REVERT: C 626 MET cc_start: 0.8160 (mtm) cc_final: 0.7588 (mtm) REVERT: C 645 LEU cc_start: 0.9406 (tp) cc_final: 0.8917 (tp) REVERT: C 648 GLU cc_start: 0.9226 (pp20) cc_final: 0.8714 (pm20) REVERT: C 657 GLU cc_start: 0.9224 (mp0) cc_final: 0.8619 (mp0) REVERT: D 36 TRP cc_start: 0.8584 (m100) cc_final: 0.8228 (m-10) REVERT: D 57 THR cc_start: 0.7880 (m) cc_final: 0.7579 (m) REVERT: D 67 PHE cc_start: 0.8650 (p90) cc_final: 0.7619 (p90) REVERT: D 71 ARG cc_start: 0.8525 (ttt-90) cc_final: 0.8226 (tmt-80) REVERT: D 89 MET cc_start: 0.8107 (mmp) cc_final: 0.6585 (tpt) REVERT: D 91 TYR cc_start: 0.8710 (m-80) cc_final: 0.8380 (m-80) REVERT: D 98 THR cc_start: 0.9393 (p) cc_final: 0.9100 (t) REVERT: E 37 GLN cc_start: 0.7722 (pp30) cc_final: 0.7428 (pp30) REVERT: E 38 GLN cc_start: 0.8498 (pt0) cc_final: 0.7993 (pt0) REVERT: E 45 LYS cc_start: 0.9037 (tptp) cc_final: 0.8788 (ttpp) REVERT: E 82 ASP cc_start: 0.9005 (m-30) cc_final: 0.8778 (m-30) REVERT: F 573 ILE cc_start: 0.9164 (pt) cc_final: 0.8846 (pt) REVERT: F 584 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8765 (tm-30) REVERT: F 621 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 624 ASP cc_start: 0.8847 (m-30) cc_final: 0.8602 (m-30) REVERT: F 648 GLU cc_start: 0.9155 (pp20) cc_final: 0.8620 (pm20) REVERT: F 658 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8724 (tm-30) REVERT: G 98 ASN cc_start: 0.8666 (t0) cc_final: 0.8016 (t0) REVERT: G 104 MET cc_start: 0.9173 (ttp) cc_final: 0.8784 (mtp) REVERT: G 114 GLN cc_start: 0.9477 (tm-30) cc_final: 0.9139 (tm-30) REVERT: G 150 MET cc_start: 0.9112 (tmm) cc_final: 0.8854 (tmm) REVERT: G 434 MET cc_start: 0.8242 (tmm) cc_final: 0.7923 (tmm) REVERT: H 1 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8172 (pm20) REVERT: H 47 TRP cc_start: 0.6752 (m-90) cc_final: 0.6367 (m-90) REVERT: H 67 PHE cc_start: 0.8719 (p90) cc_final: 0.7950 (p90) REVERT: H 72 ASP cc_start: 0.8950 (t70) cc_final: 0.8728 (t0) REVERT: I 59 LYS cc_start: 0.8035 (tptp) cc_final: 0.7791 (tptp) REVERT: I 98 ASN cc_start: 0.8256 (t0) cc_final: 0.7781 (t0) REVERT: I 102 GLU cc_start: 0.9317 (mp0) cc_final: 0.8980 (mp0) REVERT: I 114 GLN cc_start: 0.9523 (tm-30) cc_final: 0.9085 (tm-30) REVERT: I 180 ASP cc_start: 0.8853 (m-30) cc_final: 0.8649 (m-30) REVERT: I 205 CYS cc_start: 0.7241 (t) cc_final: 0.7010 (t) REVERT: I 217 TYR cc_start: 0.7715 (m-80) cc_final: 0.7069 (m-80) REVERT: I 252 LYS cc_start: 0.9333 (mtmm) cc_final: 0.9053 (mmmm) REVERT: J 29 PHE cc_start: 0.8955 (t80) cc_final: 0.8701 (t80) REVERT: J 36 TRP cc_start: 0.8395 (m100) cc_final: 0.7919 (m100) REVERT: J 44 ARG cc_start: 0.6245 (mmt180) cc_final: 0.5412 (mmt-90) REVERT: J 57 THR cc_start: 0.7741 (m) cc_final: 0.6915 (m) REVERT: J 67 PHE cc_start: 0.8600 (p90) cc_final: 0.7900 (p90) REVERT: K 21 ILE cc_start: 0.9395 (pt) cc_final: 0.9186 (pt) REVERT: K 37 GLN cc_start: 0.7290 (pp30) cc_final: 0.7020 (pp30) REVERT: K 45 LYS cc_start: 0.9191 (tptm) cc_final: 0.8862 (ttpp) REVERT: K 103 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8280 (mtmm) REVERT: L 37 GLN cc_start: 0.8161 (pp30) cc_final: 0.7937 (pp30) REVERT: L 103 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8477 (mmmm) outliers start: 4 outliers final: 0 residues processed: 497 average time/residue: 0.3125 time to fit residues: 241.6772 Evaluate side-chains 402 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 61 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.069329 restraints weight = 68335.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.071530 restraints weight = 37388.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.073023 restraints weight = 25014.793| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20587 Z= 0.231 Angle : 0.856 14.366 27934 Z= 0.420 Chirality : 0.055 0.693 3337 Planarity : 0.005 0.060 3463 Dihedral : 9.845 86.937 4330 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.08 % Favored : 83.84 % Rotamer: Outliers : 0.14 % Allowed : 0.33 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.43 % 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: -3.64 (0.15), residues: 2388 helix: -0.84 (0.27), residues: 369 sheet: -1.36 (0.27), residues: 369 loop : -3.32 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP K 35 HIS 0.009 0.002 HIS L 76 PHE 0.020 0.001 PHE J 29 TYR 0.039 0.002 TYR J 58 ARG 0.006 0.001 ARG H 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 507 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 617 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7975 (mtm-85) REVERT: A 626 MET cc_start: 0.8217 (mtm) cc_final: 0.8011 (mtm) REVERT: A 647 GLU cc_start: 0.8934 (pp20) cc_final: 0.8668 (pp20) REVERT: A 648 GLU cc_start: 0.9140 (pp20) cc_final: 0.8596 (pp20) REVERT: A 652 GLN cc_start: 0.9010 (mm110) cc_final: 0.8732 (mp10) REVERT: A 658 GLN cc_start: 0.9237 (tt0) cc_final: 0.8807 (tm-30) REVERT: B 98 ASN cc_start: 0.8283 (t0) cc_final: 0.7560 (t0) REVERT: B 121 LYS cc_start: 0.9290 (ttmt) cc_final: 0.9065 (ttpp) REVERT: B 150 MET cc_start: 0.9211 (tmm) cc_final: 0.8921 (tmm) REVERT: B 427 TRP cc_start: 0.8863 (m100) cc_final: 0.8567 (m100) REVERT: B 479 TRP cc_start: 0.9290 (m-90) cc_final: 0.8816 (m-90) REVERT: C 584 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 621 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7943 (tm-30) REVERT: C 622 ILE cc_start: 0.9245 (pt) cc_final: 0.8871 (pt) REVERT: C 626 MET cc_start: 0.8089 (mtm) cc_final: 0.7516 (mtm) REVERT: C 645 LEU cc_start: 0.9382 (tp) cc_final: 0.8908 (tp) REVERT: C 648 GLU cc_start: 0.9214 (pp20) cc_final: 0.8699 (pm20) REVERT: C 657 GLU cc_start: 0.9235 (mp0) cc_final: 0.8593 (mp0) REVERT: D 22 CYS cc_start: 0.8920 (t) cc_final: 0.8325 (t) REVERT: D 36 TRP cc_start: 0.8490 (m100) cc_final: 0.8210 (m-10) REVERT: D 44 ARG cc_start: 0.5769 (mmt-90) cc_final: 0.4414 (mmt-90) REVERT: D 57 THR cc_start: 0.7694 (m) cc_final: 0.7327 (m) REVERT: D 67 PHE cc_start: 0.8629 (p90) cc_final: 0.7554 (p90) REVERT: D 71 ARG cc_start: 0.8506 (ttt-90) cc_final: 0.8206 (tmt-80) REVERT: D 85 GLU cc_start: 0.8625 (pp20) cc_final: 0.8344 (pp20) REVERT: D 91 TYR cc_start: 0.8528 (m-80) cc_final: 0.7848 (m-10) REVERT: D 98 THR cc_start: 0.9368 (p) cc_final: 0.9066 (t) REVERT: E 24 LYS cc_start: 0.8738 (pptt) cc_final: 0.8530 (pptt) REVERT: E 37 GLN cc_start: 0.7691 (pp30) cc_final: 0.7330 (pp30) REVERT: E 38 GLN cc_start: 0.8476 (pt0) cc_final: 0.8070 (pt0) REVERT: E 87 TYR cc_start: 0.8271 (m-80) cc_final: 0.7976 (m-80) REVERT: F 573 ILE cc_start: 0.9113 (pt) cc_final: 0.8849 (pt) REVERT: F 577 GLN cc_start: 0.9143 (mt0) cc_final: 0.8819 (mt0) REVERT: F 584 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8701 (tm-30) REVERT: F 621 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8306 (tm-30) REVERT: F 624 ASP cc_start: 0.8841 (m-30) cc_final: 0.8607 (m-30) REVERT: F 645 LEU cc_start: 0.9260 (tp) cc_final: 0.8782 (tp) REVERT: F 648 GLU cc_start: 0.9152 (pp20) cc_final: 0.8614 (pm20) REVERT: F 658 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8705 (tm-30) REVERT: G 98 ASN cc_start: 0.8808 (t0) cc_final: 0.7878 (t0) REVERT: G 102 GLU cc_start: 0.9259 (mp0) cc_final: 0.8845 (mp0) REVERT: G 104 MET cc_start: 0.9050 (ttp) cc_final: 0.8443 (mtp) REVERT: G 114 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9104 (tm-30) REVERT: G 150 MET cc_start: 0.9090 (tmm) cc_final: 0.8835 (tmm) REVERT: G 302 ASN cc_start: 0.8225 (t0) cc_final: 0.8014 (t0) REVERT: G 434 MET cc_start: 0.8237 (tmm) cc_final: 0.7860 (tmm) REVERT: G 475 MET cc_start: 0.7336 (tmm) cc_final: 0.5422 (tpp) REVERT: H 1 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8233 (pm20) REVERT: H 13 LYS cc_start: 0.8969 (tppt) cc_final: 0.8682 (tppt) REVERT: H 67 PHE cc_start: 0.8654 (p90) cc_final: 0.7766 (p90) REVERT: H 72 ASP cc_start: 0.8950 (t70) cc_final: 0.8734 (t0) REVERT: I 59 LYS cc_start: 0.8002 (tptp) cc_final: 0.7763 (tptp) REVERT: I 98 ASN cc_start: 0.8285 (t0) cc_final: 0.8010 (t0) REVERT: I 102 GLU cc_start: 0.9306 (mp0) cc_final: 0.8968 (mp0) REVERT: I 114 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9028 (tm-30) REVERT: I 205 CYS cc_start: 0.7249 (t) cc_final: 0.7036 (t) REVERT: I 252 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9033 (mmmm) REVERT: I 475 MET cc_start: 0.6879 (tmm) cc_final: 0.5117 (tpp) REVERT: J 22 CYS cc_start: 0.8716 (t) cc_final: 0.8467 (t) REVERT: J 29 PHE cc_start: 0.8933 (t80) cc_final: 0.8653 (t80) REVERT: J 36 TRP cc_start: 0.8411 (m100) cc_final: 0.7936 (m100) REVERT: J 57 THR cc_start: 0.8051 (m) cc_final: 0.7365 (m) REVERT: J 67 PHE cc_start: 0.8472 (p90) cc_final: 0.7693 (p90) REVERT: J 102 TYR cc_start: 0.9142 (m-80) cc_final: 0.8800 (m-80) REVERT: K 33 MET cc_start: 0.6682 (ptt) cc_final: 0.6370 (ptt) REVERT: K 37 GLN cc_start: 0.7206 (pp30) cc_final: 0.6933 (pp30) REVERT: K 45 LYS cc_start: 0.9154 (tptm) cc_final: 0.8815 (ttpp) REVERT: K 72 THR cc_start: 0.8162 (p) cc_final: 0.7959 (p) REVERT: K 87 TYR cc_start: 0.8431 (m-80) cc_final: 0.8143 (m-80) REVERT: K 103 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8267 (mtmm) REVERT: L 33 MET cc_start: 0.6646 (pmm) cc_final: 0.6414 (pmm) REVERT: L 37 GLN cc_start: 0.8131 (pp30) cc_final: 0.7829 (pp30) REVERT: L 103 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8158 (mtmm) outliers start: 3 outliers final: 0 residues processed: 507 average time/residue: 0.3119 time to fit residues: 244.2172 Evaluate side-chains 409 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2335 > 50: distance: 88 - 131: 32.128 distance: 91 - 128: 31.540 distance: 112 - 114: 34.651 distance: 114 - 115: 47.010 distance: 115 - 116: 56.302 distance: 115 - 118: 56.847 distance: 116 - 117: 6.163 distance: 116 - 123: 60.765 distance: 118 - 119: 47.510 distance: 119 - 120: 31.363 distance: 120 - 121: 50.455 distance: 120 - 122: 52.582 distance: 123 - 124: 41.706 distance: 124 - 125: 5.135 distance: 124 - 127: 3.481 distance: 125 - 126: 24.237 distance: 125 - 128: 39.133 distance: 128 - 129: 39.169 distance: 129 - 130: 16.902 distance: 129 - 132: 52.639 distance: 130 - 131: 42.176 distance: 130 - 136: 51.258 distance: 132 - 133: 29.644 distance: 133 - 134: 38.346 distance: 134 - 135: 31.573 distance: 136 - 137: 14.121 distance: 137 - 138: 40.093 distance: 137 - 140: 22.836 distance: 138 - 139: 39.921 distance: 138 - 148: 23.948 distance: 140 - 141: 15.224 distance: 141 - 142: 19.166 distance: 141 - 143: 30.797 distance: 142 - 144: 28.461 distance: 143 - 145: 14.429 distance: 144 - 146: 37.733 distance: 145 - 146: 4.104 distance: 146 - 147: 23.368 distance: 148 - 149: 21.411 distance: 149 - 150: 31.286 distance: 149 - 152: 59.015 distance: 150 - 151: 45.393 distance: 150 - 153: 41.777 distance: 153 - 154: 40.651 distance: 153 - 159: 52.220 distance: 154 - 155: 38.779 distance: 154 - 157: 48.718 distance: 155 - 156: 63.237 distance: 155 - 160: 41.508 distance: 157 - 158: 16.565 distance: 158 - 159: 45.044 distance: 160 - 161: 56.216 distance: 160 - 166: 49.644 distance: 161 - 162: 40.823 distance: 161 - 164: 43.275 distance: 162 - 163: 42.193 distance: 162 - 167: 43.860 distance: 164 - 165: 49.949 distance: 165 - 166: 39.641 distance: 167 - 168: 23.912 distance: 168 - 169: 40.719 distance: 168 - 171: 46.246 distance: 169 - 170: 25.630 distance: 169 - 175: 60.719 distance: 171 - 172: 51.544 distance: 171 - 173: 31.398 distance: 172 - 174: 57.527 distance: 175 - 176: 10.046 distance: 176 - 177: 15.168 distance: 176 - 179: 16.085 distance: 177 - 178: 67.581 distance: 177 - 184: 52.484 distance: 179 - 180: 42.665 distance: 181 - 182: 52.178 distance: 181 - 183: 41.139 distance: 184 - 185: 44.212 distance: 185 - 186: 13.000 distance: 186 - 187: 10.350 distance: 186 - 188: 34.070