Starting phenix.real_space_refine on Thu Mar 5 19:49:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493.map" model { file = "/net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ugp_26493/03_2026/7ugp_26493_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 146 5.16 5 C 15685 2.51 5 N 4284 2.21 5 O 4932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25047 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3488 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "R" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "K" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 778 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.85, per 1000 atoms: 0.23 Number of scatterers: 25047 At special positions: 0 Unit cell: (147.73, 157.289, 151.206, 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 146 16.00 O 4932 8.00 N 4284 7.00 C 15685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=1.73 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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=2, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-4 " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 6 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 363 " " NAG A 608 " - " ASN A 234 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 160 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 448 " " NAG B 603 " - " ASN B 133 " " NAG B 604 " - " ASN B 276 " " NAG B 605 " - " ASN B 301 " " NAG B 606 " - " ASN B 392 " " NAG B 607 " - " ASN B 363 " " NAG B 608 " - " ASN B 234 " " NAG B 609 " - " ASN B 295 " " NAG B 610 " - " ASN B 160 " " NAG C 601 " - " ASN C 88 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 234 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 160 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN B 332 " " NAG W 1 " - " ASN B 156 " " NAG X 1 " - " ASN B 262 " " NAG Y 1 " - " ASN C 262 " " NAG Y 3 " - " ASN C 448 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5694 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 62 sheets defined 14.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.454A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.068A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.101A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.980A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.085A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.845A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 546 removed outlier: 3.806A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 removed outlier: 3.879A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.715A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 529 through 535 removed outlier: 4.144A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 546 removed outlier: 3.923A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER E 546 " --> pdb=" O ARG E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 595 removed outlier: 3.862A pdb=" N ILE E 573 " --> pdb=" O THR E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.678A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 658 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 538 through 546 removed outlier: 4.007A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 removed outlier: 3.905A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.751A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 659 Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.547A pdb=" N ASN M 64 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 100D through 100H removed outlier: 3.662A pdb=" N GLY M 100H" --> pdb=" O VAL M 100E" (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 64 removed outlier: 3.500A pdb=" N ASN N 64 " --> pdb=" O PRO N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 100D through 100H removed outlier: 3.569A pdb=" N GLY N 100H" --> pdb=" O VAL N 100E" (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.781A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.791A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.807A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.780A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.012A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.164A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.875A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.636A pdb=" N MET A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.198A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 3.547A pdb=" N ALA B 497 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.022A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.136A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 261 removed outlier: 5.863A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.217A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.752A pdb=" N LEU B 285 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.217A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 307 Processing sheet with id=AC2, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.182A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.546A pdb=" N ALA C 497 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR F 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 46 Processing sheet with id=AC5, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.044A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AC7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.130A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.784A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.425A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.738A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 285 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 11.054A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.425A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.202A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.678A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.678A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER M 100O" --> pdb=" O ARG M 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 20 through 23 removed outlier: 4.077A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR N 107 " --> pdb=" O TYR N 90 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR N 107 " --> pdb=" O TYR N 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER N 100O" --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE N 100K" --> pdb=" O ARG N 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.985A pdb=" N VAL N 20 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP O 34 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.723A pdb=" N THR O 107 " --> pdb=" O TYR O 90 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY O 98 " --> pdb=" O TYR O 100M" (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE O 100K" --> pdb=" O ARG O 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 20 through 22 removed outlier: 4.110A pdb=" N VAL O 20 " --> pdb=" O LEU O 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N THR G 110 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 94 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.798A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.791A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.791A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.704A pdb=" N ARG P 9 " --> pdb=" O ARG P 103 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR P 105 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 19 through 21 Processing sheet with id=AF8, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.861A pdb=" N ARG Q 9 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR Q 105 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 19 through 21 Processing sheet with id=AG1, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.742A pdb=" N ARG R 9 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR R 105 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 19 through 21 Processing sheet with id=AG3, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.505A pdb=" N ILE J 20 " --> pdb=" O LEU J 75 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER J 74 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 47 through 48 removed outlier: 3.782A pdb=" N TYR J 38 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.775A pdb=" N ILE K 20 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU K 75 " --> pdb=" O ILE K 20 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER K 74 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 47 through 48 removed outlier: 3.765A pdb=" N TYR K 38 " --> pdb=" O TYR K 89 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.751A pdb=" N ILE L 20 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU L 75 " --> pdb=" O ILE L 20 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 47 through 48 removed outlier: 3.513A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) 776 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7919 1.34 - 1.47: 6342 1.47 - 1.59: 11112 1.59 - 1.71: 9 1.71 - 1.83: 202 Bond restraints: 25584 Sorted by residual: bond pdb=" C1 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.399 1.513 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C1 MAN Z 4 " pdb=" C2 MAN Z 4 " ideal model delta sigma weight residual 1.526 1.640 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.598 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 25579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 33581 2.42 - 4.84: 971 4.84 - 7.26: 157 7.26 - 9.68: 35 9.68 - 12.10: 15 Bond angle restraints: 34759 Sorted by residual: angle pdb=" C THR N 83 " pdb=" N PRO N 84 " pdb=" CA PRO N 84 " ideal model delta sigma weight residual 119.05 128.95 -9.90 1.11e+00 8.12e-01 7.96e+01 angle pdb=" C ASN A 188 " pdb=" N THR A 189 " pdb=" CA THR A 189 " ideal model delta sigma weight residual 122.61 133.37 -10.76 1.56e+00 4.11e-01 4.76e+01 angle pdb=" C LYS B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta sigma weight residual 118.85 125.15 -6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" C LYS C 117 " pdb=" N PRO C 118 " pdb=" CA PRO C 118 " ideal model delta sigma weight residual 118.85 124.99 -6.14 1.09e+00 8.42e-01 3.18e+01 angle pdb=" C GLU B 267 " pdb=" N GLU B 268 " pdb=" CA GLU B 268 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 ... (remaining 34754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 14896 22.50 - 45.00: 945 45.00 - 67.50: 149 67.50 - 90.00: 60 90.00 - 112.51: 32 Dihedral angle restraints: 16082 sinusoidal: 7196 harmonic: 8886 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 162.59 -69.59 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.70 54.70 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA CYS A 119 " pdb=" C CYS A 119 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 16079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3880 0.146 - 0.292: 139 0.292 - 0.439: 16 0.439 - 0.585: 7 0.585 - 0.731: 3 Chirality restraints: 4045 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C2 NAG Y 1 " pdb=" C1 NAG Y 1 " pdb=" C3 NAG Y 1 " pdb=" N2 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.88 -0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 262 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.76e+00 ... (remaining 4042 not shown) Planarity restraints: 4399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 49 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C TYR R 49 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 49 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN R 50 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 46 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C LEU R 46 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 46 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 47 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR O 83 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO O 84 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO O 84 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 84 " 0.040 5.00e-02 4.00e+02 ... (remaining 4396 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 1 1.65 - 2.46: 99 2.46 - 3.27: 22781 3.27 - 4.09: 60984 4.09 - 4.90: 105978 Warning: very small nonbonded interaction distances. Nonbonded interactions: 189843 Sorted by model distance: nonbonded pdb=" CD2 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 0.835 3.340 nonbonded pdb=" CG TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.782 3.260 nonbonded pdb=" CE2 TYR R 49 " pdb=" OD2 ASP R 53 " model vdw 1.888 3.340 nonbonded pdb=" CD2 TYR R 49 " pdb=" CG ASP R 53 " model vdw 1.915 3.570 nonbonded pdb=" O ALA E 526 " pdb=" CG2 THR E 627 " model vdw 2.020 3.460 ... (remaining 189838 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' and resid 32 through 609) selection = (chain 'B' and resid 32 through 609) selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 523 through 529 or (resid 530 and (name N or name CA or na \ me C or name O or name CB )) or resid 531 through 701)) selection = (chain 'F' and (resid 523 through 529 or (resid 530 and (name N or name CA or na \ me C or name O or name CB )) or resid 531 through 701)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 108)) selection = (chain 'Q' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 108)) selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'Z' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'U' selection = chain 'X' } 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.298 25686 Z= 0.345 Angle : 1.139 48.849 35024 Z= 0.583 Chirality : 0.070 0.731 4045 Planarity : 0.007 0.073 4358 Dihedral : 16.081 112.506 10283 Min Nonbonded Distance : 0.835 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.52 % Allowed : 8.43 % Favored : 91.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.12), residues: 3036 helix: -3.82 (0.12), residues: 336 sheet: -2.47 (0.15), residues: 900 loop : -3.14 (0.11), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 585 TYR 0.013 0.001 TYR M 100B PHE 0.019 0.002 PHE A 159 TRP 0.010 0.001 TRP D 628 HIS 0.012 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00648 (25584) covalent geometry : angle 0.99545 (34759) SS BOND : bond 0.05060 ( 35) SS BOND : angle 6.97891 ( 70) hydrogen bonds : bond 0.22356 ( 698) hydrogen bonds : angle 9.28755 ( 2055) Misc. bond : bond 0.00906 ( 2) link_ALPHA1-2 : bond 0.00840 ( 3) link_ALPHA1-2 : angle 1.92392 ( 9) link_ALPHA1-4 : bond 0.03736 ( 3) link_ALPHA1-4 : angle 10.31789 ( 9) link_ALPHA1-6 : bond 0.01354 ( 3) link_ALPHA1-6 : angle 3.30484 ( 9) link_BETA1-4 : bond 0.01151 ( 15) link_BETA1-4 : angle 5.21705 ( 45) link_NAG-ASN : bond 0.01031 ( 41) link_NAG-ASN : angle 6.52118 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 374 time to evaluate : 1.174 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: B 191 TYR cc_start: 0.8069 (m-80) cc_final: 0.7826 (m-80) REVERT: B 475 MET cc_start: 0.6523 (mpp) cc_final: 0.5949 (mmt) REVERT: C 189 THR cc_start: 0.4330 (OUTLIER) cc_final: 0.4066 (t) REVERT: O 31 ASN cc_start: 0.6013 (t0) cc_final: 0.5746 (p0) REVERT: O 90 TYR cc_start: 0.8426 (m-80) cc_final: 0.8181 (m-80) REVERT: O 100 MET cc_start: 0.6872 (mpp) cc_final: 0.6533 (mpp) REVERT: G 98 LEU cc_start: 0.8746 (mt) cc_final: 0.8403 (mt) REVERT: H 98 LEU cc_start: 0.8516 (mt) cc_final: 0.8208 (mt) REVERT: I 98 LEU cc_start: 0.8755 (mt) cc_final: 0.8391 (mt) REVERT: P 85 ASP cc_start: 0.7293 (t0) cc_final: 0.7020 (t0) REVERT: P 86 TYR cc_start: 0.6881 (m-80) cc_final: 0.6658 (m-80) REVERT: R 85 ASP cc_start: 0.7125 (t0) cc_final: 0.6893 (t0) REVERT: R 86 TYR cc_start: 0.7047 (m-80) cc_final: 0.6812 (m-80) REVERT: K 18 VAL cc_start: 0.3362 (m) cc_final: 0.3113 (p) REVERT: K 68 LYS cc_start: 0.2774 (mtpt) cc_final: 0.2283 (tptt) REVERT: L 68 LYS cc_start: 0.3785 (mttt) cc_final: 0.2887 (tptm) outliers start: 14 outliers final: 3 residues processed: 388 average time/residue: 0.1982 time to fit residues: 113.8833 Evaluate side-chains 193 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 6.9990 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 99 ASN A 103 GLN A 258 GLN A 279 ASN A 302 ASN B 72 HIS B 99 ASN B 103 GLN B 258 GLN B 279 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 103 GLN C 258 GLN C 302 ASN C 348 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 6 GLN I 6 GLN P 51 ASN Q 51 ASN R 34 GLN R 51 ASN J 40 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 40 GLN L 33 ASN L 40 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.061036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048269 restraints weight = 144378.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049648 restraints weight = 86648.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049897 restraints weight = 55520.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050119 restraints weight = 47274.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050152 restraints weight = 43940.054| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25686 Z= 0.191 Angle : 0.783 19.893 35024 Z= 0.363 Chirality : 0.052 0.456 4045 Planarity : 0.005 0.062 4358 Dihedral : 12.089 113.159 4706 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3036 helix: -0.60 (0.25), residues: 354 sheet: -2.26 (0.15), residues: 939 loop : -2.71 (0.12), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 56 TYR 0.016 0.001 TYR H 27 PHE 0.027 0.002 PHE C 223 TRP 0.015 0.001 TRP I 103 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00422 (25584) covalent geometry : angle 0.69705 (34759) SS BOND : bond 0.00616 ( 35) SS BOND : angle 1.57262 ( 70) hydrogen bonds : bond 0.03765 ( 698) hydrogen bonds : angle 6.38871 ( 2055) Misc. bond : bond 0.00187 ( 2) link_ALPHA1-2 : bond 0.01430 ( 3) link_ALPHA1-2 : angle 3.09243 ( 9) link_ALPHA1-4 : bond 0.02521 ( 3) link_ALPHA1-4 : angle 8.16129 ( 9) link_ALPHA1-6 : bond 0.01349 ( 3) link_ALPHA1-6 : angle 3.31188 ( 9) link_BETA1-4 : bond 0.00896 ( 15) link_BETA1-4 : angle 3.69989 ( 45) link_NAG-ASN : bond 0.00602 ( 41) link_NAG-ASN : angle 4.93168 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 237 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8069 (m-10) cc_final: 0.7718 (m-80) REVERT: A 426 MET cc_start: 0.8293 (tpt) cc_final: 0.7756 (tpp) REVERT: B 191 TYR cc_start: 0.8402 (m-80) cc_final: 0.8161 (m-80) REVERT: M 3 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7409 (pp30) REVERT: M 47 TRP cc_start: 0.7507 (t60) cc_final: 0.7030 (t-100) REVERT: M 80 LEU cc_start: 0.6558 (tp) cc_final: 0.6324 (tt) REVERT: N 3 GLN cc_start: 0.7468 (tp40) cc_final: 0.6391 (pp30) REVERT: N 100 MET cc_start: 0.6101 (mpp) cc_final: 0.5730 (mpp) REVERT: O 31 ASN cc_start: 0.6999 (t0) cc_final: 0.6166 (p0) REVERT: O 47 TRP cc_start: 0.7308 (t60) cc_final: 0.6817 (t-100) REVERT: O 81 LYS cc_start: 0.8490 (mttp) cc_final: 0.7964 (mmtt) REVERT: O 90 TYR cc_start: 0.8201 (m-80) cc_final: 0.7734 (m-80) REVERT: O 100 MET cc_start: 0.7154 (mpp) cc_final: 0.6299 (mpp) REVERT: G 10 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6745 (tp30) REVERT: G 80 MET cc_start: 0.7761 (tmm) cc_final: 0.7536 (tmm) REVERT: I 80 MET cc_start: 0.7768 (tmm) cc_final: 0.7464 (tmm) REVERT: P 85 ASP cc_start: 0.7983 (t0) cc_final: 0.7646 (t0) REVERT: P 86 TYR cc_start: 0.7885 (m-80) cc_final: 0.7651 (m-80) REVERT: Q 46 LEU cc_start: 0.6568 (tp) cc_final: 0.6213 (tp) REVERT: K 68 LYS cc_start: 0.3073 (mtpt) cc_final: 0.2762 (tptt) REVERT: K 102 LEU cc_start: 0.6631 (mt) cc_final: 0.6352 (mt) REVERT: L 68 LYS cc_start: 0.4263 (mttt) cc_final: 0.3033 (tptm) REVERT: L 88 TYR cc_start: 0.6031 (m-80) cc_final: 0.5781 (m-80) outliers start: 7 outliers final: 2 residues processed: 244 average time/residue: 0.1848 time to fit residues: 69.5307 Evaluate side-chains 170 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 12 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 285 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 197 ASN B 103 GLN B 195 ASN B 279 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS C 279 ASN C 330 HIS C 425 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN N 39 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 ASN P 51 ASN Q 38 HIS Q 50 ASN Q 51 ASN K 39 GLN K 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046312 restraints weight = 145189.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047622 restraints weight = 85810.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047790 restraints weight = 54132.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048141 restraints weight = 49815.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048191 restraints weight = 44495.851| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25686 Z= 0.191 Angle : 0.771 19.904 35024 Z= 0.356 Chirality : 0.052 0.459 4045 Planarity : 0.004 0.055 4358 Dihedral : 10.558 114.135 4706 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.14), residues: 3036 helix: 0.61 (0.28), residues: 354 sheet: -2.07 (0.15), residues: 966 loop : -2.55 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 419 TYR 0.020 0.001 TYR K 34 PHE 0.012 0.002 PHE B 317 TRP 0.014 0.001 TRP N 34 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00420 (25584) covalent geometry : angle 0.68438 (34759) SS BOND : bond 0.00424 ( 35) SS BOND : angle 1.76070 ( 70) hydrogen bonds : bond 0.03731 ( 698) hydrogen bonds : angle 5.94333 ( 2055) Misc. bond : bond 0.00133 ( 2) link_ALPHA1-2 : bond 0.01310 ( 3) link_ALPHA1-2 : angle 2.33471 ( 9) link_ALPHA1-4 : bond 0.02568 ( 3) link_ALPHA1-4 : angle 8.41247 ( 9) link_ALPHA1-6 : bond 0.01405 ( 3) link_ALPHA1-6 : angle 4.30366 ( 9) link_BETA1-4 : bond 0.00778 ( 15) link_BETA1-4 : angle 3.73156 ( 45) link_NAG-ASN : bond 0.00628 ( 41) link_NAG-ASN : angle 4.81108 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 THR cc_start: 0.8597 (t) cc_final: 0.8336 (p) REVERT: A 475 MET cc_start: 0.7072 (mtm) cc_final: 0.6738 (mtt) REVERT: B 191 TYR cc_start: 0.8591 (m-80) cc_final: 0.8328 (m-80) REVERT: M 3 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7352 (pp30) REVERT: M 47 TRP cc_start: 0.7584 (t60) cc_final: 0.7225 (t-100) REVERT: N 3 GLN cc_start: 0.7389 (tp40) cc_final: 0.6284 (pp30) REVERT: O 47 TRP cc_start: 0.7289 (t60) cc_final: 0.6995 (t60) REVERT: O 100 MET cc_start: 0.7183 (mpp) cc_final: 0.6873 (mpp) REVERT: G 10 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6914 (tp30) REVERT: G 80 MET cc_start: 0.7811 (tmm) cc_final: 0.7544 (tmm) REVERT: H 80 MET cc_start: 0.7534 (tmm) cc_final: 0.7265 (tmm) REVERT: I 80 MET cc_start: 0.7840 (tmm) cc_final: 0.7461 (tmm) REVERT: P 9 ARG cc_start: 0.7319 (ptm-80) cc_final: 0.6730 (ptp90) REVERT: P 85 ASP cc_start: 0.7911 (t0) cc_final: 0.7580 (t0) REVERT: P 86 TYR cc_start: 0.7901 (m-80) cc_final: 0.7635 (m-80) REVERT: R 85 ASP cc_start: 0.7503 (t0) cc_final: 0.7234 (t0) REVERT: K 68 LYS cc_start: 0.2993 (mtpt) cc_final: 0.2727 (tptt) REVERT: K 88 TYR cc_start: 0.5608 (m-80) cc_final: 0.5390 (m-80) REVERT: L 68 LYS cc_start: 0.4209 (mttt) cc_final: 0.2957 (tptt) REVERT: L 102 LEU cc_start: 0.6778 (mt) cc_final: 0.6466 (mp) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.1713 time to fit residues: 58.7946 Evaluate side-chains 166 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 215 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 288 optimal weight: 0.0770 chunk 163 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 267 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 302 ASN B 330 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS C 330 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS H 32 HIS I 6 GLN I 32 HIS P 51 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN J 39 GLN L 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.059457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047487 restraints weight = 144974.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048040 restraints weight = 92061.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.048348 restraints weight = 64208.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048518 restraints weight = 59657.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048561 restraints weight = 55832.003| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25686 Z= 0.239 Angle : 0.819 19.189 35024 Z= 0.380 Chirality : 0.053 0.461 4045 Planarity : 0.004 0.056 4358 Dihedral : 10.298 117.950 4706 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.14), residues: 3036 helix: 0.75 (0.28), residues: 357 sheet: -1.99 (0.16), residues: 951 loop : -2.51 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 8 TYR 0.022 0.002 TYR A 191 PHE 0.016 0.002 PHE C 53 TRP 0.014 0.002 TRP B 427 HIS 0.020 0.002 HIS Q 89 Details of bonding type rmsd covalent geometry : bond 0.00532 (25584) covalent geometry : angle 0.73671 (34759) SS BOND : bond 0.00426 ( 35) SS BOND : angle 2.07951 ( 70) hydrogen bonds : bond 0.03675 ( 698) hydrogen bonds : angle 5.92987 ( 2055) Misc. bond : bond 0.00082 ( 2) link_ALPHA1-2 : bond 0.01128 ( 3) link_ALPHA1-2 : angle 2.99656 ( 9) link_ALPHA1-4 : bond 0.02417 ( 3) link_ALPHA1-4 : angle 7.96830 ( 9) link_ALPHA1-6 : bond 0.00506 ( 3) link_ALPHA1-6 : angle 1.32696 ( 9) link_BETA1-4 : bond 0.00705 ( 15) link_BETA1-4 : angle 3.99034 ( 45) link_NAG-ASN : bond 0.00749 ( 41) link_NAG-ASN : angle 4.88642 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 THR cc_start: 0.8719 (t) cc_final: 0.8431 (p) REVERT: B 475 MET cc_start: 0.8174 (ptp) cc_final: 0.7596 (ptp) REVERT: C 426 MET cc_start: 0.8121 (tpp) cc_final: 0.7678 (tpt) REVERT: C 475 MET cc_start: 0.8172 (ptp) cc_final: 0.7830 (ptp) REVERT: M 3 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7431 (pp30) REVERT: M 27 ASP cc_start: 0.6332 (p0) cc_final: 0.6000 (p0) REVERT: M 47 TRP cc_start: 0.7908 (t60) cc_final: 0.7509 (t-100) REVERT: N 81 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7496 (mppt) REVERT: O 27 ASP cc_start: 0.6000 (p0) cc_final: 0.5529 (p0) REVERT: O 100 MET cc_start: 0.7090 (mpp) cc_final: 0.6782 (mpp) REVERT: G 80 MET cc_start: 0.7826 (tmm) cc_final: 0.7513 (tmm) REVERT: H 80 MET cc_start: 0.7541 (tmm) cc_final: 0.7213 (tmm) REVERT: I 80 MET cc_start: 0.7834 (tmm) cc_final: 0.7508 (tmm) REVERT: P 85 ASP cc_start: 0.7838 (t0) cc_final: 0.7629 (t0) REVERT: Q 46 LEU cc_start: 0.6787 (tp) cc_final: 0.6423 (tp) REVERT: K 62 ASP cc_start: 0.7027 (t0) cc_final: 0.6487 (t0) REVERT: K 68 LYS cc_start: 0.3551 (mtpt) cc_final: 0.3057 (tptt) REVERT: K 88 TYR cc_start: 0.5398 (m-80) cc_final: 0.5164 (m-80) REVERT: K 102 LEU cc_start: 0.6696 (mt) cc_final: 0.6326 (mp) REVERT: L 23 THR cc_start: 0.8645 (t) cc_final: 0.8432 (p) REVERT: L 62 ASP cc_start: 0.7345 (t0) cc_final: 0.6734 (t0) REVERT: L 68 LYS cc_start: 0.4080 (mttt) cc_final: 0.2851 (tptt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1555 time to fit residues: 53.4457 Evaluate side-chains 162 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 0.0370 chunk 124 optimal weight: 0.0570 chunk 279 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 181 optimal weight: 0.0470 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 195 ASN A 197 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 377 ASN C 425 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 51 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 51 ASN L 41 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.058854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.046313 restraints weight = 142327.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047437 restraints weight = 79348.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.048144 restraints weight = 54186.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048576 restraints weight = 42649.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048789 restraints weight = 36952.047| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25686 Z= 0.133 Angle : 0.719 19.445 35024 Z= 0.329 Chirality : 0.051 0.463 4045 Planarity : 0.004 0.051 4358 Dihedral : 9.704 114.500 4706 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 3036 helix: 1.16 (0.29), residues: 360 sheet: -1.85 (0.16), residues: 939 loop : -2.30 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 54 TYR 0.017 0.001 TYR A 191 PHE 0.019 0.001 PHE I 100F TRP 0.019 0.001 TRP O 47 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (25584) covalent geometry : angle 0.63776 (34759) SS BOND : bond 0.00303 ( 35) SS BOND : angle 1.64708 ( 70) hydrogen bonds : bond 0.03148 ( 698) hydrogen bonds : angle 5.61283 ( 2055) Misc. bond : bond 0.00150 ( 2) link_ALPHA1-2 : bond 0.01502 ( 3) link_ALPHA1-2 : angle 2.47670 ( 9) link_ALPHA1-4 : bond 0.02695 ( 3) link_ALPHA1-4 : angle 8.30216 ( 9) link_ALPHA1-6 : bond 0.00300 ( 3) link_ALPHA1-6 : angle 1.67048 ( 9) link_BETA1-4 : bond 0.00770 ( 15) link_BETA1-4 : angle 3.50496 ( 45) link_NAG-ASN : bond 0.00603 ( 41) link_NAG-ASN : angle 4.54644 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 426 MET cc_start: 0.8408 (tpt) cc_final: 0.7985 (tpp) REVERT: B 475 MET cc_start: 0.8148 (ptp) cc_final: 0.7386 (ptp) REVERT: C 426 MET cc_start: 0.7953 (tpp) cc_final: 0.7709 (tpt) REVERT: C 464 THR cc_start: 0.8508 (t) cc_final: 0.8283 (p) REVERT: M 3 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7325 (pp30) REVERT: M 27 ASP cc_start: 0.6278 (p0) cc_final: 0.5912 (p0) REVERT: M 47 TRP cc_start: 0.7800 (t60) cc_final: 0.7364 (t-100) REVERT: N 45 LEU cc_start: 0.7351 (mm) cc_final: 0.7115 (mp) REVERT: N 81 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7528 (mppt) REVERT: O 27 ASP cc_start: 0.5895 (p0) cc_final: 0.5358 (p0) REVERT: O 81 LYS cc_start: 0.8267 (mttp) cc_final: 0.7751 (mmtt) REVERT: O 100 MET cc_start: 0.7073 (mpp) cc_final: 0.6761 (mpp) REVERT: G 80 MET cc_start: 0.7804 (tmm) cc_final: 0.7584 (tmm) REVERT: H 80 MET cc_start: 0.7644 (tmm) cc_final: 0.7354 (tmm) REVERT: I 80 MET cc_start: 0.7895 (tmm) cc_final: 0.7503 (tmm) REVERT: Q 46 LEU cc_start: 0.6813 (tp) cc_final: 0.6399 (tp) REVERT: J 49 MET cc_start: 0.7875 (mmm) cc_final: 0.7578 (mmm) REVERT: K 62 ASP cc_start: 0.7058 (t0) cc_final: 0.6550 (t0) REVERT: K 68 LYS cc_start: 0.3297 (mtpt) cc_final: 0.2858 (tptt) REVERT: K 102 LEU cc_start: 0.6628 (mt) cc_final: 0.6252 (mp) REVERT: L 62 ASP cc_start: 0.7307 (t0) cc_final: 0.6706 (t0) REVERT: L 68 LYS cc_start: 0.4001 (mttt) cc_final: 0.2729 (tptt) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1562 time to fit residues: 55.9066 Evaluate side-chains 162 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 48 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 77 GLN P 51 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN Q 51 ASN L 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054648 restraints weight = 117951.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054846 restraints weight = 97093.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.054934 restraints weight = 87528.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055047 restraints weight = 80612.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055005 restraints weight = 73539.881| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 25686 Z= 0.290 Angle : 0.867 19.201 35024 Z= 0.405 Chirality : 0.054 0.466 4045 Planarity : 0.005 0.081 4358 Dihedral : 10.302 121.173 4706 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.14), residues: 3036 helix: 0.79 (0.28), residues: 363 sheet: -1.93 (0.16), residues: 957 loop : -2.37 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 38 TYR 0.036 0.002 TYR L 88 PHE 0.018 0.002 PHE B 383 TRP 0.023 0.002 TRP O 47 HIS 0.019 0.002 HIS R 89 Details of bonding type rmsd covalent geometry : bond 0.00651 (25584) covalent geometry : angle 0.78891 (34759) SS BOND : bond 0.00588 ( 35) SS BOND : angle 1.83233 ( 70) hydrogen bonds : bond 0.03867 ( 698) hydrogen bonds : angle 5.93392 ( 2055) Misc. bond : bond 0.00059 ( 2) link_ALPHA1-2 : bond 0.01401 ( 3) link_ALPHA1-2 : angle 3.61734 ( 9) link_ALPHA1-4 : bond 0.02554 ( 3) link_ALPHA1-4 : angle 7.97481 ( 9) link_ALPHA1-6 : bond 0.00365 ( 3) link_ALPHA1-6 : angle 1.69509 ( 9) link_BETA1-4 : bond 0.00546 ( 15) link_BETA1-4 : angle 3.99855 ( 45) link_NAG-ASN : bond 0.00792 ( 41) link_NAG-ASN : angle 4.97831 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8372 (tpp) cc_final: 0.8105 (tpp) REVERT: A 475 MET cc_start: 0.8135 (ptp) cc_final: 0.7581 (ptp) REVERT: B 475 MET cc_start: 0.8172 (ptp) cc_final: 0.7948 (ptp) REVERT: C 426 MET cc_start: 0.8128 (tpp) cc_final: 0.7839 (tpt) REVERT: E 657 GLU cc_start: 0.8325 (pm20) cc_final: 0.8107 (pm20) REVERT: M 3 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7392 (pp30) REVERT: M 27 ASP cc_start: 0.6579 (p0) cc_final: 0.6115 (p0) REVERT: M 47 TRP cc_start: 0.8057 (t60) cc_final: 0.7682 (t-100) REVERT: N 100 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8413 (mt-10) REVERT: O 27 ASP cc_start: 0.6146 (p0) cc_final: 0.5638 (p0) REVERT: O 81 LYS cc_start: 0.8257 (mttp) cc_final: 0.7806 (mmtt) REVERT: H 80 MET cc_start: 0.7684 (tmm) cc_final: 0.7317 (tmm) REVERT: I 80 MET cc_start: 0.7735 (tmm) cc_final: 0.7393 (tmm) REVERT: J 49 MET cc_start: 0.8025 (mmm) cc_final: 0.7743 (mmm) REVERT: J 62 ASP cc_start: 0.7457 (t70) cc_final: 0.6754 (t0) REVERT: J 85 GLU cc_start: 0.6928 (pm20) cc_final: 0.6509 (pp20) REVERT: K 62 ASP cc_start: 0.7472 (t0) cc_final: 0.7112 (t0) REVERT: K 68 LYS cc_start: 0.3609 (mtpt) cc_final: 0.2969 (tptt) REVERT: L 62 ASP cc_start: 0.7511 (t0) cc_final: 0.7062 (t0) REVERT: L 68 LYS cc_start: 0.4250 (mttt) cc_final: 0.2899 (tptt) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.1529 time to fit residues: 49.5745 Evaluate side-chains 157 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 193 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 192 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 51 ASN Q 51 ASN L 33 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.057981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045436 restraints weight = 143043.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.046547 restraints weight = 79133.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047248 restraints weight = 53865.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047673 restraints weight = 42430.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.047914 restraints weight = 36797.503| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25686 Z= 0.175 Angle : 0.766 19.309 35024 Z= 0.353 Chirality : 0.052 0.465 4045 Planarity : 0.004 0.044 4358 Dihedral : 9.813 115.903 4706 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.04 % Allowed : 1.39 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.15), residues: 3036 helix: 1.12 (0.28), residues: 363 sheet: -1.89 (0.16), residues: 990 loop : -2.23 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 54 TYR 0.014 0.001 TYR H 27 PHE 0.014 0.001 PHE B 376 TRP 0.026 0.001 TRP O 47 HIS 0.008 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00390 (25584) covalent geometry : angle 0.68722 (34759) SS BOND : bond 0.00366 ( 35) SS BOND : angle 1.78809 ( 70) hydrogen bonds : bond 0.03324 ( 698) hydrogen bonds : angle 5.74788 ( 2055) Misc. bond : bond 0.00135 ( 2) link_ALPHA1-2 : bond 0.01438 ( 3) link_ALPHA1-2 : angle 2.90125 ( 9) link_ALPHA1-4 : bond 0.02605 ( 3) link_ALPHA1-4 : angle 8.05580 ( 9) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 1.60028 ( 9) link_BETA1-4 : bond 0.00736 ( 15) link_BETA1-4 : angle 3.56613 ( 45) link_NAG-ASN : bond 0.00585 ( 41) link_NAG-ASN : angle 4.64522 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8371 (tpp) cc_final: 0.8012 (tpp) REVERT: A 475 MET cc_start: 0.8004 (ptp) cc_final: 0.7531 (ptp) REVERT: B 351 LYS cc_start: 0.8698 (tmmt) cc_final: 0.8338 (tmtt) REVERT: C 464 THR cc_start: 0.8544 (t) cc_final: 0.8304 (p) REVERT: M 3 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7480 (pp30) REVERT: M 27 ASP cc_start: 0.6629 (p0) cc_final: 0.6173 (p0) REVERT: M 47 TRP cc_start: 0.8102 (t60) cc_final: 0.7893 (t-100) REVERT: O 27 ASP cc_start: 0.6110 (p0) cc_final: 0.5568 (p0) REVERT: O 48 ILE cc_start: 0.9056 (pt) cc_final: 0.8703 (mp) REVERT: O 81 LYS cc_start: 0.8154 (mttp) cc_final: 0.7685 (mmtt) REVERT: O 100 MET cc_start: 0.7034 (mpp) cc_final: 0.6680 (mpp) REVERT: G 80 MET cc_start: 0.7816 (tmm) cc_final: 0.7542 (tmm) REVERT: H 69 MET cc_start: 0.7978 (mtt) cc_final: 0.7751 (mtm) REVERT: H 80 MET cc_start: 0.7751 (tmm) cc_final: 0.7479 (tmm) REVERT: I 80 MET cc_start: 0.8010 (tmm) cc_final: 0.7571 (tmm) REVERT: J 62 ASP cc_start: 0.7524 (t70) cc_final: 0.6798 (t0) REVERT: J 85 GLU cc_start: 0.6603 (pm20) cc_final: 0.6367 (pp20) REVERT: K 62 ASP cc_start: 0.7270 (t0) cc_final: 0.7006 (t0) REVERT: K 68 LYS cc_start: 0.3704 (mtpt) cc_final: 0.3071 (tptt) REVERT: L 62 ASP cc_start: 0.7575 (t0) cc_final: 0.7117 (t0) REVERT: L 68 LYS cc_start: 0.4023 (mttt) cc_final: 0.2675 (tptt) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.1567 time to fit residues: 51.6128 Evaluate side-chains 159 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 269 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 57 optimal weight: 0.0050 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 51 ASN Q 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056009 restraints weight = 104726.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056330 restraints weight = 91965.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056249 restraints weight = 82017.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056206 restraints weight = 79114.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056233 restraints weight = 77547.404| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25686 Z= 0.201 Angle : 0.789 19.094 35024 Z= 0.364 Chirality : 0.052 0.480 4045 Planarity : 0.004 0.050 4358 Dihedral : 9.841 118.660 4706 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.04 % Allowed : 0.86 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 3036 helix: 1.15 (0.28), residues: 360 sheet: -1.84 (0.16), residues: 957 loop : -2.32 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 38 TYR 0.018 0.001 TYR H 27 PHE 0.013 0.002 PHE B 376 TRP 0.043 0.002 TRP F 631 HIS 0.006 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00448 (25584) covalent geometry : angle 0.71191 (34759) SS BOND : bond 0.00367 ( 35) SS BOND : angle 1.72519 ( 70) hydrogen bonds : bond 0.03409 ( 698) hydrogen bonds : angle 5.74300 ( 2055) Misc. bond : bond 0.00099 ( 2) link_ALPHA1-2 : bond 0.01465 ( 3) link_ALPHA1-2 : angle 3.32057 ( 9) link_ALPHA1-4 : bond 0.02562 ( 3) link_ALPHA1-4 : angle 7.95909 ( 9) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 1.59390 ( 9) link_BETA1-4 : bond 0.00633 ( 15) link_BETA1-4 : angle 3.67773 ( 45) link_NAG-ASN : bond 0.00641 ( 41) link_NAG-ASN : angle 4.66689 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 426 MET cc_start: 0.8368 (tpp) cc_final: 0.8027 (tpp) REVERT: A 475 MET cc_start: 0.8014 (ptp) cc_final: 0.7475 (ptp) REVERT: B 351 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8453 (tmtt) REVERT: C 464 THR cc_start: 0.8666 (t) cc_final: 0.8394 (p) REVERT: M 3 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7492 (pp30) REVERT: M 27 ASP cc_start: 0.6495 (p0) cc_final: 0.6050 (p0) REVERT: O 27 ASP cc_start: 0.6119 (p0) cc_final: 0.5557 (p0) REVERT: O 80 LEU cc_start: 0.7064 (tp) cc_final: 0.6836 (tp) REVERT: O 81 LYS cc_start: 0.8196 (mttp) cc_final: 0.7706 (mmtt) REVERT: O 100 MET cc_start: 0.6761 (mpp) cc_final: 0.6527 (mpp) REVERT: G 80 MET cc_start: 0.7782 (tmm) cc_final: 0.7544 (tmm) REVERT: H 80 MET cc_start: 0.7625 (tmm) cc_final: 0.7337 (tmm) REVERT: I 80 MET cc_start: 0.7754 (tmm) cc_final: 0.7387 (tmm) REVERT: J 62 ASP cc_start: 0.7599 (t70) cc_final: 0.6911 (t0) REVERT: J 85 GLU cc_start: 0.6626 (pm20) cc_final: 0.6378 (pp20) REVERT: K 68 LYS cc_start: 0.3517 (mtpt) cc_final: 0.2913 (tptt) REVERT: K 102 LEU cc_start: 0.7377 (mt) cc_final: 0.7114 (mt) REVERT: L 62 ASP cc_start: 0.7561 (t0) cc_final: 0.7277 (t0) REVERT: L 68 LYS cc_start: 0.3961 (mttt) cc_final: 0.2630 (tptt) outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.1607 time to fit residues: 50.6472 Evaluate side-chains 158 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 215 optimal weight: 0.4980 chunk 252 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 183 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 72 HIS C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.059009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046531 restraints weight = 143173.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047659 restraints weight = 78831.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.048374 restraints weight = 53741.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048798 restraints weight = 42266.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049070 restraints weight = 36693.374| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25686 Z= 0.119 Angle : 0.722 19.166 35024 Z= 0.329 Chirality : 0.050 0.491 4045 Planarity : 0.004 0.042 4358 Dihedral : 9.269 113.209 4706 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.15), residues: 3036 helix: 1.87 (0.29), residues: 345 sheet: -1.68 (0.16), residues: 933 loop : -2.11 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 54 TYR 0.011 0.001 TYR L 51 PHE 0.014 0.001 PHE B 376 TRP 0.036 0.001 TRP F 631 HIS 0.004 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00258 (25584) covalent geometry : angle 0.65013 (34759) SS BOND : bond 0.00322 ( 35) SS BOND : angle 1.34552 ( 70) hydrogen bonds : bond 0.02977 ( 698) hydrogen bonds : angle 5.45954 ( 2055) Misc. bond : bond 0.00164 ( 2) link_ALPHA1-2 : bond 0.01671 ( 3) link_ALPHA1-2 : angle 2.61942 ( 9) link_ALPHA1-4 : bond 0.02863 ( 3) link_ALPHA1-4 : angle 8.38711 ( 9) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 1.58679 ( 9) link_BETA1-4 : bond 0.00827 ( 15) link_BETA1-4 : angle 3.24650 ( 45) link_NAG-ASN : bond 0.00625 ( 41) link_NAG-ASN : angle 4.25850 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8473 (m-80) cc_final: 0.8104 (m-80) REVERT: A 426 MET cc_start: 0.8252 (tpp) cc_final: 0.7882 (tpp) REVERT: A 475 MET cc_start: 0.7873 (ptp) cc_final: 0.7132 (ptp) REVERT: B 351 LYS cc_start: 0.8644 (tmmt) cc_final: 0.8307 (tmtt) REVERT: M 3 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7548 (pp30) REVERT: M 27 ASP cc_start: 0.6545 (p0) cc_final: 0.6059 (p0) REVERT: O 27 ASP cc_start: 0.6087 (p0) cc_final: 0.5497 (p0) REVERT: O 80 LEU cc_start: 0.6801 (tp) cc_final: 0.6355 (tt) REVERT: O 81 LYS cc_start: 0.8089 (mttp) cc_final: 0.7571 (mmtt) REVERT: O 100 MET cc_start: 0.7022 (mpp) cc_final: 0.6590 (mpp) REVERT: G 80 MET cc_start: 0.7872 (tmm) cc_final: 0.7546 (tmm) REVERT: I 80 MET cc_start: 0.7933 (tmm) cc_final: 0.7575 (tmm) REVERT: I 87 THR cc_start: 0.6663 (p) cc_final: 0.6433 (p) REVERT: Q 60 GLU cc_start: 0.8066 (pm20) cc_final: 0.7654 (mm-30) REVERT: R 17 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6455 (mm-30) REVERT: J 62 ASP cc_start: 0.7531 (t70) cc_final: 0.6782 (t0) REVERT: K 68 LYS cc_start: 0.3878 (mtpt) cc_final: 0.3143 (tptt) REVERT: K 88 TYR cc_start: 0.5592 (m-80) cc_final: 0.5292 (m-80) REVERT: L 62 ASP cc_start: 0.7625 (t0) cc_final: 0.7135 (t0) REVERT: L 68 LYS cc_start: 0.4103 (mttt) cc_final: 0.2669 (tptt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1562 time to fit residues: 52.1298 Evaluate side-chains 158 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 209 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 330 HIS B 72 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 72 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 51 ASN Q 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.060247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047801 restraints weight = 143315.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048928 restraints weight = 79409.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.049636 restraints weight = 54160.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050056 restraints weight = 42627.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.050316 restraints weight = 37015.591| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25686 Z= 0.125 Angle : 0.723 18.898 35024 Z= 0.328 Chirality : 0.050 0.470 4045 Planarity : 0.004 0.043 4358 Dihedral : 9.192 116.179 4706 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.04 % Allowed : 0.07 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 3036 helix: 1.94 (0.29), residues: 345 sheet: -1.59 (0.16), residues: 954 loop : -2.01 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 62 TYR 0.012 0.001 TYR H 27 PHE 0.012 0.001 PHE B 376 TRP 0.033 0.001 TRP F 631 HIS 0.005 0.001 HIS Q 38 Details of bonding type rmsd covalent geometry : bond 0.00276 (25584) covalent geometry : angle 0.65094 (34759) SS BOND : bond 0.00320 ( 35) SS BOND : angle 1.55270 ( 70) hydrogen bonds : bond 0.02950 ( 698) hydrogen bonds : angle 5.31922 ( 2055) Misc. bond : bond 0.00132 ( 2) link_ALPHA1-2 : bond 0.01675 ( 3) link_ALPHA1-2 : angle 2.95794 ( 9) link_ALPHA1-4 : bond 0.02865 ( 3) link_ALPHA1-4 : angle 8.23120 ( 9) link_ALPHA1-6 : bond 0.00312 ( 3) link_ALPHA1-6 : angle 1.55959 ( 9) link_BETA1-4 : bond 0.00686 ( 15) link_BETA1-4 : angle 3.30146 ( 45) link_NAG-ASN : bond 0.00614 ( 41) link_NAG-ASN : angle 4.24636 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8485 (m-80) cc_final: 0.8080 (m-80) REVERT: A 426 MET cc_start: 0.8315 (tpp) cc_final: 0.7940 (tpp) REVERT: A 475 MET cc_start: 0.7828 (ptp) cc_final: 0.7078 (ptp) REVERT: B 351 LYS cc_start: 0.8648 (tmmt) cc_final: 0.8303 (tmtt) REVERT: M 3 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7572 (pp30) REVERT: M 27 ASP cc_start: 0.6568 (p0) cc_final: 0.6059 (p0) REVERT: M 43 LYS cc_start: 0.7646 (pttp) cc_final: 0.6878 (tptt) REVERT: N 81 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7387 (mttp) REVERT: O 27 ASP cc_start: 0.6178 (p0) cc_final: 0.5613 (p0) REVERT: O 38 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7757 (tmm-80) REVERT: O 47 TRP cc_start: 0.8347 (t60) cc_final: 0.7908 (t60) REVERT: O 80 LEU cc_start: 0.6686 (tp) cc_final: 0.6436 (tp) REVERT: O 81 LYS cc_start: 0.8116 (mttp) cc_final: 0.7662 (mmtt) REVERT: O 100 MET cc_start: 0.7086 (mpp) cc_final: 0.6680 (mpp) REVERT: G 80 MET cc_start: 0.7827 (tmm) cc_final: 0.7560 (tmm) REVERT: H 87 THR cc_start: 0.6723 (p) cc_final: 0.6473 (p) REVERT: I 80 MET cc_start: 0.7946 (tmm) cc_final: 0.7568 (tmm) REVERT: I 98 LEU cc_start: 0.8616 (mt) cc_final: 0.8410 (mt) REVERT: J 62 ASP cc_start: 0.7550 (t70) cc_final: 0.6801 (t0) REVERT: K 68 LYS cc_start: 0.3882 (mtpt) cc_final: 0.3141 (tptt) REVERT: K 88 TYR cc_start: 0.5606 (m-80) cc_final: 0.5275 (m-80) REVERT: L 62 ASP cc_start: 0.7662 (t0) cc_final: 0.7132 (t0) REVERT: L 68 LYS cc_start: 0.4142 (mttt) cc_final: 0.2696 (tptt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1502 time to fit residues: 47.8906 Evaluate side-chains 159 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 227 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 chunk 46 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 302 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 72 HIS B 195 ASN C 67 ASN C 72 HIS ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.057010 restraints weight = 94622.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057013 restraints weight = 82706.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057013 restraints weight = 77147.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057013 restraints weight = 77147.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057013 restraints weight = 77147.285| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25686 Z= 0.244 Angle : 0.828 18.841 35024 Z= 0.384 Chirality : 0.053 0.463 4045 Planarity : 0.004 0.044 4358 Dihedral : 9.750 120.517 4706 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.15), residues: 3036 helix: 1.26 (0.28), residues: 360 sheet: -1.72 (0.16), residues: 993 loop : -2.17 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 500 TYR 0.021 0.002 TYR H 27 PHE 0.014 0.002 PHE B 383 TRP 0.026 0.002 TRP F 631 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00544 (25584) covalent geometry : angle 0.75510 (34759) SS BOND : bond 0.00423 ( 35) SS BOND : angle 2.01969 ( 70) hydrogen bonds : bond 0.03543 ( 698) hydrogen bonds : angle 5.56625 ( 2055) Misc. bond : bond 0.00080 ( 2) link_ALPHA1-2 : bond 0.01286 ( 3) link_ALPHA1-2 : angle 3.76364 ( 9) link_ALPHA1-4 : bond 0.02606 ( 3) link_ALPHA1-4 : angle 7.86956 ( 9) link_ALPHA1-6 : bond 0.00353 ( 3) link_ALPHA1-6 : angle 1.64754 ( 9) link_BETA1-4 : bond 0.00594 ( 15) link_BETA1-4 : angle 3.72053 ( 45) link_NAG-ASN : bond 0.00691 ( 41) link_NAG-ASN : angle 4.57642 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.58 seconds wall clock time: 63 minutes 36.30 seconds (3816.30 seconds total)