Starting phenix.real_space_refine on Sun Jul 5 02:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp1_27628/07_2026/8dp1_27628.cif" } resolution = 3.46 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= 0.003 sd= 0.136 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 135 5.16 5 C 15645 2.51 5 N 4212 2.21 5 O 5008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25000 Number of models: 1 Model: "" Number of chains: 33 Chain: "M" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "R" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "S" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "W" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "E" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "F" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "H" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "J" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "N" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "O" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "Q" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" 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 chiralities: 3 Chain: "D" 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 chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "K" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "L" 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 chiralities: 3 Chain: "P" 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 3 Chain: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.06, per 1000 atoms: 0.20 Number of scatterers: 25000 At special positions: 0 Unit cell: (184.68, 194.4, 159.84, 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 135 16.00 O 5008 8.00 N 4212 7.00 C 15645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " distance=2.04 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 199 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 208 " distance=2.03 Simple disulfide: pdb=" SG CYS S 598 " - pdb=" SG CYS S 604 " distance=2.03 Simple disulfide: pdb=" SG CYS S 605 " - pdb=" SG CYS W 501 " distance=2.04 Simple disulfide: pdb=" SG CYS W 54 " - pdb=" SG CYS W 74 " distance=2.04 Simple disulfide: pdb=" SG CYS W 119 " - pdb=" SG CYS W 205 " distance=2.03 Simple disulfide: pdb=" SG CYS W 126 " - pdb=" SG CYS W 196 " distance=2.04 Simple disulfide: pdb=" SG CYS W 131 " - pdb=" SG CYS W 157 " distance=2.03 Simple disulfide: pdb=" SG CYS W 218 " - pdb=" SG CYS W 247 " distance=2.03 Simple disulfide: pdb=" SG CYS W 228 " - pdb=" SG CYS W 239 " distance=2.04 Simple disulfide: pdb=" SG CYS W 296 " - pdb=" SG CYS W 331 " distance=2.04 Simple disulfide: pdb=" SG CYS W 378 " - pdb=" SG CYS W 445 " distance=2.04 Simple disulfide: pdb=" SG CYS W 385 " - pdb=" SG CYS W 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS H 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 208 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.04 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.04 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS Q 605 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 152 " - pdb=" SG CYS N 208 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.05 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 598 " - pdb=" SG CYS Q 604 " 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=0, symmetry=0 Links applied ALPHA1-2 " MAN A 4 " - " MAN A 5 " " MAN A 5 " - " MAN A 6 " " MAN A 8 " - " MAN A 9 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA A 3 " - " MAN A 4 " " MAN A 7 " - " MAN A 10 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 10 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 10 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA A 3 " - " MAN A 7 " " MAN A 7 " - " MAN A 8 " " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG P 1 " - " NAG P 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 1 " - " ASN W 332 " " NAG B 601 " - " ASN B 133 " " NAG B 602 " - " ASN B 160 " " NAG B 603 " - " ASN B 197 " " NAG B 604 " - " ASN B 234 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 355 " " NAG B 607 " - " ASN B 363 " " NAG B 608 " - " ASN B 386 " " NAG C 1 " - " ASN W 262 " " NAG D 1 " - " ASN W 156 " " NAG G 1 " - " ASN W 301 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 625 " " NAG H 703 " - " ASN H 637 " " NAG I 1 " - " ASN W 295 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 160 " " NAG J 603 " - " ASN J 197 " " NAG J 604 " - " ASN J 234 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 355 " " NAG J 607 " - " ASN J 363 " " NAG J 608 " - " ASN J 386 " " NAG L 1 " - " ASN B 156 " " NAG P 1 " - " ASN B 295 " " NAG Q 701 " - " ASN Q 611 " " NAG Q 702 " - " ASN Q 625 " " NAG Q 703 " - " ASN Q 637 " " NAG S 701 " - " ASN S 611 " " NAG S 702 " - " ASN S 625 " " NAG S 703 " - " ASN S 637 " " NAG T 1 " - " ASN B 301 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN J 332 " " NAG W 601 " - " ASN W 133 " " NAG W 602 " - " ASN W 160 " " NAG W 603 " - " ASN W 197 " " NAG W 604 " - " ASN W 234 " " NAG W 605 " - " ASN W 276 " " NAG W 606 " - " ASN W 355 " " NAG W 607 " - " ASN W 363 " " NAG W 608 " - " ASN W 386 " " NAG X 1 " - " ASN J 156 " " NAG Y 1 " - " ASN J 295 " " NAG Z 1 " - " ASN J 301 " " NAG a 1 " - " ASN J 262 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5652 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 18.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'M' and resid 84 through 88 Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'M' and resid 188 through 193 Processing helix chain 'R' and resid 28 through 30 No H-bonds generated for 'chain 'R' and resid 28 through 30' Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 139 through 145 Processing helix chain 'R' and resid 199 through 201 No H-bonds generated for 'chain 'R' and resid 199 through 201' Processing helix chain 'S' and resid 529 through 534 Processing helix chain 'S' and resid 536 through 542 removed outlier: 4.316A pdb=" N GLN S 540 " --> pdb=" O THR S 536 " (cutoff:3.500A) Processing helix chain 'S' and resid 569 through 596 removed outlier: 3.543A pdb=" N LEU S 581 " --> pdb=" O GLN S 577 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL S 583 " --> pdb=" O ARG S 579 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU S 593 " --> pdb=" O ASP S 589 " (cutoff:3.500A) Processing helix chain 'S' and resid 619 through 624 Processing helix chain 'S' and resid 627 through 636 Processing helix chain 'S' and resid 638 through 662 removed outlier: 3.505A pdb=" N ILE S 642 " --> pdb=" O TYR S 638 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 74 Processing helix chain 'W' and resid 99 through 117 Processing helix chain 'W' and resid 122 through 126 Processing helix chain 'W' and resid 141 through 152 Processing helix chain 'W' and resid 334 through 354 removed outlier: 4.124A pdb=" N LYS W 351 " --> pdb=" O LYS W 347 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS W 352 " --> pdb=" O GLN W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 368 through 373 Processing helix chain 'W' and resid 387 through 390 Processing helix chain 'W' and resid 475 through 484 removed outlier: 3.959A pdb=" N TRP W 479 " --> pdb=" O MET W 475 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER W 481 " --> pdb=" O ASP W 477 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU W 482 " --> pdb=" O ASN W 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.393A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.811A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.615A pdb=" N VAL F 88 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 537 through 542 Processing helix chain 'H' and resid 569 through 596 removed outlier: 3.521A pdb=" N VAL H 580 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 593 " --> pdb=" O ASP H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 624 Processing helix chain 'H' and resid 627 through 636 Processing helix chain 'H' and resid 638 through 662 removed outlier: 3.501A pdb=" N LYS H 655 " --> pdb=" O ASN H 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 74 Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.513A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 152 Processing helix chain 'J' and resid 195 through 198 Processing helix chain 'J' and resid 335 through 353 removed outlier: 4.407A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 387 through 390 Processing helix chain 'J' and resid 475 through 484 removed outlier: 3.897A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER J 481 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 30 No H-bonds generated for 'chain 'N' and resid 28 through 30' Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 199 through 201 No H-bonds generated for 'chain 'N' and resid 199 through 201' Processing helix chain 'O' and resid 84 through 88 removed outlier: 3.666A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 131 Processing helix chain 'O' and resid 188 through 193 Processing helix chain 'Q' and resid 529 through 534 Processing helix chain 'Q' and resid 536 through 542 removed outlier: 4.177A pdb=" N GLN Q 540 " --> pdb=" O THR Q 536 " (cutoff:3.500A) Processing helix chain 'Q' and resid 569 through 596 removed outlier: 3.603A pdb=" N LEU Q 593 " --> pdb=" O ASP Q 589 " (cutoff:3.500A) Processing helix chain 'Q' and resid 618 through 624 removed outlier: 3.702A pdb=" N ILE Q 622 " --> pdb=" O ASN Q 618 " (cutoff:3.500A) Processing helix chain 'Q' and resid 627 through 636 removed outlier: 3.620A pdb=" N GLU Q 634 " --> pdb=" O GLN Q 630 " (cutoff:3.500A) Processing helix chain 'Q' and resid 638 through 662 removed outlier: 3.755A pdb=" N GLY Q 644 " --> pdb=" O GLN Q 640 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA Q 662 " --> pdb=" O GLN Q 658 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 13 current: chain 'M' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 58 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'M' and resid 119 through 123 removed outlier: 4.227A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR M 178 " --> pdb=" O ASN M 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 158 through 159 Processing sheet with id=AA5, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'R' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 11 through 12 current: chain 'R' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 58 through 60 current: chain 'R' and resid 106 through 107 Processing sheet with id=AA7, first strand: chain 'R' and resid 132 through 136 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 147 through 157 current: chain 'R' and resid 188 through 197 Processing sheet with id=AA8, first strand: chain 'R' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'S' and resid 603 through 609 removed outlier: 3.584A pdb=" N THR S 606 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL W 36 " --> pdb=" O THR S 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'W' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'W' and resid 91 through 94 removed outlier: 3.553A pdb=" N GLU W 91 " --> pdb=" O CYS W 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'W' and resid 200 through 203 removed outlier: 6.553A pdb=" N ALA W 200 " --> pdb=" O ALA W 433 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR W 435 " --> pdb=" O ALA W 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR W 202 " --> pdb=" O TYR W 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'W' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 259 through 261 current: chain 'W' and resid 284 through 312 removed outlier: 6.730A pdb=" N ASN W 301 " --> pdb=" O ILE W 322 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE W 322 " --> pdb=" O ASN W 301 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR W 303 " --> pdb=" O GLY W 321 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN W 315 " --> pdb=" O ILE W 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 315 through 323 current: chain 'W' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 381 through 385 current: chain 'W' and resid 466 through 470 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.475A pdb=" N VAL B 36 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.618A pdb=" N PHE B 93 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.442A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 312 removed outlier: 6.591A pdb=" N ASN B 301 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE B 322 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 323 current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 60 current: chain 'E' and resid 106 through 107 Processing sheet with id=AC7, first strand: chain 'E' and resid 132 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 147 through 157 current: chain 'E' and resid 188 through 197 Processing sheet with id=AC8, first strand: chain 'E' and resid 163 through 166 removed outlier: 3.560A pdb=" N THR E 217 " --> pdb=" O HIS E 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 13 current: chain 'F' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 59 current: chain 'F' and resid 102 through 103 Processing sheet with id=AD2, first strand: chain 'F' and resid 119 through 123 removed outlier: 4.239A pdb=" N VAL F 138 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AD4, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.625A pdb=" N VAL J 36 " --> pdb=" O THR Q 606 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR Q 606 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.567A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'J' and resid 66 through 67 removed outlier: 7.144A pdb=" N HIS J 66 " --> pdb=" O SER J 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AE1, first strand: chain 'J' and resid 200 through 203 removed outlier: 6.501A pdb=" N ALA J 200 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR J 435 " --> pdb=" O ALA J 200 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.700A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323 current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 466 through 470 Processing sheet with id=AE3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'N' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 12 current: chain 'N' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 58 through 60 current: chain 'N' and resid 106 through 107 Processing sheet with id=AE5, first strand: chain 'N' and resid 132 through 136 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 147 through 157 current: chain 'N' and resid 188 through 197 Processing sheet with id=AE6, first strand: chain 'N' and resid 163 through 166 Processing sheet with id=AE7, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'O' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 13 current: chain 'O' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 58 through 59 current: chain 'O' and resid 102 through 103 Processing sheet with id=AE9, first strand: chain 'O' and resid 119 through 123 removed outlier: 4.245A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR O 178 " --> pdb=" O ASN O 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 158 through 159 removed outlier: 3.502A pdb=" N LYS O 212 " --> pdb=" O CYS O 199 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 1884 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: 4.07 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6720 1.33 - 1.46: 4532 1.46 - 1.58: 14087 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25519 Sorted by residual: bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.409 1.504 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" CA PRO W 437 " pdb=" C PRO W 437 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.55e+01 bond pdb=" C3 BMA a 3 " pdb=" O3 BMA a 3 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 MAN A 9 " pdb=" O5 MAN A 9 " ideal model delta sigma weight residual 1.399 1.478 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG J 605 " pdb=" O5 NAG J 605 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 25514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 32409 3.39 - 6.78: 2229 6.78 - 10.17: 30 10.17 - 13.56: 5 13.56 - 16.95: 1 Bond angle restraints: 34674 Sorted by residual: angle pdb=" CA THR W 123 " pdb=" CB THR W 123 " pdb=" OG1 THR W 123 " ideal model delta sigma weight residual 109.60 126.55 -16.95 1.50e+00 4.44e-01 1.28e+02 angle pdb=" CA PRO J 124 " pdb=" N PRO J 124 " pdb=" CD PRO J 124 " ideal model delta sigma weight residual 112.00 100.80 11.20 1.40e+00 5.10e-01 6.40e+01 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 112.47 125.80 -13.33 2.06e+00 2.36e-01 4.19e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 120.00 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" N ASN J 234 " pdb=" CA ASN J 234 " pdb=" CB ASN J 234 " ideal model delta sigma weight residual 110.49 102.06 8.43 1.48e+00 4.57e-01 3.24e+01 ... (remaining 34669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13394 17.96 - 35.92: 931 35.92 - 53.88: 198 53.88 - 71.85: 61 71.85 - 89.81: 32 Dihedral angle restraints: 14616 sinusoidal: 5835 harmonic: 8781 Sorted by residual: dihedral pdb=" N PRO B 124 " pdb=" C PRO B 124 " pdb=" CA PRO B 124 " pdb=" CB PRO B 124 " ideal model delta harmonic sigma weight residual 115.10 148.88 -33.78 0 2.50e+00 1.60e-01 1.83e+02 dihedral pdb=" C PRO B 124 " pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" CB PRO B 124 " ideal model delta harmonic sigma weight residual -120.70 -151.33 30.63 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" CB CYS W 378 " pdb=" SG CYS W 378 " pdb=" SG CYS W 445 " pdb=" CB CYS W 445 " ideal model delta sinusoidal sigma weight residual -86.00 -141.11 55.11 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 4135 0.294 - 0.588: 27 0.588 - 0.883: 7 0.883 - 1.177: 0 1.177 - 1.471: 4 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.77e+03 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-02 2.50e+03 4.67e+03 chirality pdb=" C1 MAN V 10 " pdb=" O3 MAN V 7 " pdb=" C2 MAN V 10 " pdb=" O5 MAN V 10 " both_signs ideal model delta sigma weight residual False 2.40 1.58 0.82 2.00e-02 2.50e+03 1.69e+03 ... (remaining 4170 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 47 " -0.237 2.00e-02 2.50e+03 1.30e-01 4.23e+02 pdb=" CG TRP N 47 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP N 47 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP N 47 " 0.130 2.00e-02 2.50e+03 pdb=" NE1 TRP N 47 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 TRP N 47 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP N 47 " 0.184 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 47 " -0.148 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 47 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP N 47 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.141 2.00e-02 2.50e+03 1.50e-01 2.82e+02 pdb=" CG ASN B 234 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG B 604 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 234 " 0.136 2.00e-02 2.50e+03 1.44e-01 2.60e+02 pdb=" CG ASN W 234 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN W 234 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN W 234 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG W 604 " 0.177 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 12605 3.00 - 3.47: 23731 3.47 - 3.95: 41771 3.95 - 4.42: 45966 4.42 - 4.90: 76798 Nonbonded interactions: 200871 Sorted by model distance: nonbonded pdb=" OH TYR R 33 " pdb=" OD1 ASP W 325 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP O 175 " pdb=" OG1 THR O 177 " model vdw 2.539 3.040 nonbonded pdb=" OG SER M 126 " pdb=" OD1 ASP M 128 " model vdw 2.540 3.040 nonbonded pdb=" OG SER O 126 " pdb=" OD1 ASP O 128 " model vdw 2.540 3.040 nonbonded pdb=" O5 BMA V 3 " pdb=" O6 BMA V 3 " model vdw 2.546 2.432 ... (remaining 200866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'K' selection = chain 'V' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'W' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'L' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'H' selection = chain 'Q' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.080 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.014 0.095 25658 Z= 0.806 Angle : 1.902 19.436 35046 Z= 1.202 Chirality : 0.118 1.471 4173 Planarity : 0.017 0.175 4302 Dihedral : 14.131 89.807 8829 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.38 % Favored : 95.02 % Rotamer: Outliers : 1.61 % Allowed : 4.08 % Favored : 94.31 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 10.20 % 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: -0.92 (0.14), residues: 2991 helix: -1.58 (0.21), residues: 405 sheet: -0.46 (0.16), residues: 909 loop : -0.32 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 100 TYR 0.201 0.025 TYR E 206 PHE 0.083 0.014 PHE J 383 TRP 0.237 0.029 TRP N 47 HIS 0.024 0.005 HIS N 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01395 / 0.81 (25519) covalent geometry : angle 1.84797 / 1.20 (34674) SS BOND : bond 0.00594 / 0.41 ( 45) SS BOND : angle 2.04820 / 1.38 ( 90) hydrogen bonds : bond 0.17152 / 11.47 ( 706) hydrogen bonds : angle 8.25201 / 5.73 ( 1884) link_ALPHA1-2 : bond 0.01056 / 0.50 ( 9) link_ALPHA1-2 : angle 4.25947 / 2.74 ( 27) link_ALPHA1-3 : bond 0.02524 / 1.23 ( 7) link_ALPHA1-3 : angle 6.04465 / 3.65 ( 21) link_ALPHA1-6 : bond 0.02556 / 1.28 ( 7) link_ALPHA1-6 : angle 6.51533 / 3.92 ( 21) link_BETA1-4 : bond 0.02525 / 1.60 ( 24) link_BETA1-4 : angle 6.45995 / 4.42 ( 72) link_NAG-ASN : bond 0.00980 / 0.61 ( 47) link_NAG-ASN : angle 4.53875 / 3.01 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 519 PHE cc_start: 0.5431 (t80) cc_final: 0.5212 (t80) REVERT: S 584 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7630 (mt-10) REVERT: W 44 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8895 (m) REVERT: W 475 MET cc_start: 0.7887 (mtt) cc_final: 0.6601 (mtt) REVERT: B 475 MET cc_start: 0.7878 (mtt) cc_final: 0.7518 (mtt) REVERT: F 42 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: O 87 ASP cc_start: 0.6422 (m-30) cc_final: 0.5864 (m-30) REVERT: O 112 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8643 (tptt) REVERT: Q 584 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7542 (mt-10) outliers start: 43 outliers final: 8 residues processed: 181 average time/residue: 0.2188 time to fit residues: 56.4906 Evaluate side-chains 86 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 396 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain O residue 113 ARG Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 448 ASN W 478 ASN B 448 ASN J 105 HIS J 428 GLN J 448 ASN O 143 ASN Q 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.049422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.035287 restraints weight = 171332.890| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.95 r_work: 0.2940 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 25658 Z= 0.167 Angle : 0.795 18.395 35046 Z= 0.384 Chirality : 0.048 0.465 4173 Planarity : 0.005 0.166 4302 Dihedral : 6.849 76.506 3294 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.82 % Rotamer: Outliers : 1.05 % Allowed : 6.85 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -0.15 (0.15), residues: 2991 helix: 0.18 (0.25), residues: 426 sheet: -0.08 (0.15), residues: 1050 loop : -0.04 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 588 TYR 0.017 0.002 TYR R 206 PHE 0.014 0.002 PHE R 178 TRP 0.027 0.002 TRP J 427 HIS 0.005 0.001 HIS J 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25519) covalent geometry : angle 0.74073 / 0.37 (34674) SS BOND : bond 0.00315 / 0.17 ( 45) SS BOND : angle 0.78734 / 0.54 ( 90) hydrogen bonds : bond 0.05964 / 4.15 ( 706) hydrogen bonds : angle 6.07316 / 4.21 ( 1884) link_ALPHA1-2 : bond 0.00490 / 0.25 ( 9) link_ALPHA1-2 : angle 2.57264 / 1.53 ( 27) link_ALPHA1-3 : bond 0.01089 / 0.59 ( 7) link_ALPHA1-3 : angle 2.47566 / 1.50 ( 21) link_ALPHA1-6 : bond 0.00685 / 0.37 ( 7) link_ALPHA1-6 : angle 1.61963 / 0.99 ( 21) link_BETA1-4 : bond 0.01846 / 1.05 ( 24) link_BETA1-4 : angle 4.70285 / 3.41 ( 72) link_NAG-ASN : bond 0.00404 / 0.27 ( 47) link_NAG-ASN : angle 2.78488 / 1.91 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: M 174 LYS cc_start: 0.8665 (pttm) cc_final: 0.7713 (mppt) REVERT: S 519 PHE cc_start: 0.5532 (t80) cc_final: 0.5023 (t80) REVERT: S 584 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8362 (mt-10) REVERT: W 475 MET cc_start: 0.8004 (mtt) cc_final: 0.7220 (mtt) REVERT: F 128 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.5753 (p0) REVERT: F 147 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6779 (tpt170) REVERT: H 519 PHE cc_start: 0.5505 (t80) cc_final: 0.5229 (t80) REVERT: J 286 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8793 (t) REVERT: J 428 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.5824 (mp10) REVERT: J 475 MET cc_start: 0.8324 (mtt) cc_final: 0.8043 (mmt) REVERT: O 4 MET cc_start: 0.7715 (mmt) cc_final: 0.7487 (mmt) REVERT: O 42 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8855 (tt0) REVERT: Q 519 PHE cc_start: 0.6768 (t80) cc_final: 0.6476 (t80) REVERT: Q 584 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8340 (mt-10) outliers start: 28 outliers final: 9 residues processed: 118 average time/residue: 0.1828 time to fit residues: 32.7155 Evaluate side-chains 82 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 166 ARG Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 428 GLN Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain O residue 113 ARG Chi-restraints excluded: chain Q residue 616 ASN Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 216 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 432 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.048396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.034123 restraints weight = 172197.963| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.00 r_work: 0.2890 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25658 Z= 0.216 Angle : 0.751 19.024 35046 Z= 0.358 Chirality : 0.049 0.458 4173 Planarity : 0.005 0.162 4302 Dihedral : 6.043 72.343 3287 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.24 % Allowed : 8.01 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.14 (0.15), residues: 2991 helix: 0.52 (0.26), residues: 426 sheet: -0.13 (0.16), residues: 1038 loop : -0.11 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 617 TYR 0.019 0.002 TYR R 33 PHE 0.014 0.002 PHE F 103 TRP 0.033 0.002 TRP W 427 HIS 0.004 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (25519) covalent geometry : angle 0.69878 / 0.35 (34674) SS BOND : bond 0.00337 / 0.20 ( 45) SS BOND : angle 0.72787 / 0.50 ( 90) hydrogen bonds : bond 0.05324 / 3.69 ( 706) hydrogen bonds : angle 5.69958 / 3.94 ( 1884) link_ALPHA1-2 : bond 0.00312 / 0.16 ( 9) link_ALPHA1-2 : angle 2.86880 / 1.67 ( 27) link_ALPHA1-3 : bond 0.01229 / 0.61 ( 7) link_ALPHA1-3 : angle 1.97732 / 1.21 ( 21) link_ALPHA1-6 : bond 0.00770 / 0.38 ( 7) link_ALPHA1-6 : angle 1.69208 / 1.00 ( 21) link_BETA1-4 : bond 0.01647 / 0.91 ( 24) link_BETA1-4 : angle 4.55857 / 3.36 ( 72) link_NAG-ASN : bond 0.00383 / 0.26 ( 47) link_NAG-ASN : angle 2.53911 / 1.72 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8976 (tt0) REVERT: M 174 LYS cc_start: 0.8690 (pttm) cc_final: 0.7792 (mppt) REVERT: S 519 PHE cc_start: 0.5563 (t80) cc_final: 0.5138 (t80) REVERT: S 584 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8401 (mt-10) REVERT: W 475 MET cc_start: 0.8121 (mtt) cc_final: 0.7765 (mtp) REVERT: F 147 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.6767 (tpt170) REVERT: H 519 PHE cc_start: 0.5536 (t80) cc_final: 0.5288 (t80) REVERT: O 4 MET cc_start: 0.8008 (mmt) cc_final: 0.7446 (mmt) REVERT: Q 519 PHE cc_start: 0.6590 (t80) cc_final: 0.6338 (t80) REVERT: Q 584 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8450 (mt-10) outliers start: 33 outliers final: 11 residues processed: 96 average time/residue: 0.1677 time to fit residues: 25.7546 Evaluate side-chains 78 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain O residue 113 ARG Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 259 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.048504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.034358 restraints weight = 171185.202| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.95 r_work: 0.2897 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 25658 Z= 0.171 Angle : 0.682 18.565 35046 Z= 0.321 Chirality : 0.046 0.447 4173 Planarity : 0.005 0.155 4302 Dihedral : 5.608 73.741 3287 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 1.20 % Allowed : 8.61 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: -0.05 (0.16), residues: 2991 helix: 0.83 (0.26), residues: 444 sheet: -0.13 (0.15), residues: 1041 loop : -0.09 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 588 TYR 0.016 0.001 TYR R 33 PHE 0.012 0.001 PHE J 468 TRP 0.033 0.002 TRP W 427 HIS 0.004 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (25519) covalent geometry : angle 0.63077 / 0.31 (34674) SS BOND : bond 0.00281 / 0.16 ( 45) SS BOND : angle 0.56021 / 0.38 ( 90) hydrogen bonds : bond 0.04516 / 3.13 ( 706) hydrogen bonds : angle 5.30823 / 3.66 ( 1884) link_ALPHA1-2 : bond 0.00340 / 0.17 ( 9) link_ALPHA1-2 : angle 2.77323 / 1.62 ( 27) link_ALPHA1-3 : bond 0.00979 / 0.51 ( 7) link_ALPHA1-3 : angle 2.00558 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00492 / 0.25 ( 7) link_ALPHA1-6 : angle 1.61210 / 0.97 ( 21) link_BETA1-4 : bond 0.01640 / 0.91 ( 24) link_BETA1-4 : angle 4.35961 / 3.23 ( 72) link_NAG-ASN : bond 0.00300 / 0.21 ( 47) link_NAG-ASN : angle 2.32476 / 1.59 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8950 (tt0) REVERT: M 174 LYS cc_start: 0.8680 (pttm) cc_final: 0.7772 (mppt) REVERT: S 519 PHE cc_start: 0.5623 (t80) cc_final: 0.5214 (t80) REVERT: S 584 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8424 (mt-10) REVERT: W 475 MET cc_start: 0.8032 (mtt) cc_final: 0.7707 (mtp) REVERT: B 475 MET cc_start: 0.7612 (mtp) cc_final: 0.6455 (mpp) REVERT: F 4 MET cc_start: 0.8205 (mmm) cc_final: 0.7738 (mmm) REVERT: F 147 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.6601 (tmt-80) REVERT: H 519 PHE cc_start: 0.5601 (t80) cc_final: 0.5375 (t80) REVERT: O 4 MET cc_start: 0.7993 (mmt) cc_final: 0.7417 (mmt) REVERT: Q 519 PHE cc_start: 0.6375 (t80) cc_final: 0.6108 (t80) REVERT: Q 584 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8396 (mt-10) outliers start: 32 outliers final: 14 residues processed: 94 average time/residue: 0.1630 time to fit residues: 24.6597 Evaluate side-chains 81 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain O residue 113 ARG Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 27 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 577 GLN ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS B 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.048110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033915 restraints weight = 170622.113| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.97 r_work: 0.2884 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25658 Z= 0.187 Angle : 0.678 18.413 35046 Z= 0.318 Chirality : 0.047 0.446 4173 Planarity : 0.005 0.156 4302 Dihedral : 5.467 72.921 3287 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.01 % Allowed : 9.70 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.01 (0.16), residues: 2991 helix: 0.99 (0.27), residues: 426 sheet: -0.17 (0.15), residues: 1056 loop : -0.03 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 588 TYR 0.016 0.001 TYR R 33 PHE 0.012 0.002 PHE J 468 TRP 0.027 0.002 TRP W 427 HIS 0.004 0.001 HIS R 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (25519) covalent geometry : angle 0.62744 / 0.31 (34674) SS BOND : bond 0.00296 / 0.17 ( 45) SS BOND : angle 0.58052 / 0.40 ( 90) hydrogen bonds : bond 0.04488 / 3.10 ( 706) hydrogen bonds : angle 5.24871 / 3.62 ( 1884) link_ALPHA1-2 : bond 0.00209 / 0.10 ( 9) link_ALPHA1-2 : angle 2.87723 / 1.68 ( 27) link_ALPHA1-3 : bond 0.01045 / 0.52 ( 7) link_ALPHA1-3 : angle 1.82824 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00550 / 0.27 ( 7) link_ALPHA1-6 : angle 1.67776 / 1.01 ( 21) link_BETA1-4 : bond 0.01535 / 0.86 ( 24) link_BETA1-4 : angle 4.32992 / 3.21 ( 72) link_NAG-ASN : bond 0.00316 / 0.22 ( 47) link_NAG-ASN : angle 2.25600 / 1.54 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: M 174 LYS cc_start: 0.8642 (pttm) cc_final: 0.8283 (pptt) REVERT: S 584 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8446 (mt-10) REVERT: W 475 MET cc_start: 0.8037 (mtt) cc_final: 0.7836 (mtp) REVERT: F 174 LYS cc_start: 0.8206 (pttm) cc_final: 0.7450 (mppt) REVERT: H 519 PHE cc_start: 0.5512 (t80) cc_final: 0.5303 (t80) REVERT: J 95 MET cc_start: 0.8632 (ptm) cc_final: 0.8076 (ttp) REVERT: J 150 MET cc_start: 0.4383 (tpt) cc_final: 0.3656 (tpt) REVERT: O 4 MET cc_start: 0.8017 (mmt) cc_final: 0.7326 (mmt) REVERT: Q 519 PHE cc_start: 0.6357 (t80) cc_final: 0.6078 (t80) REVERT: Q 584 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8451 (mt-10) outliers start: 27 outliers final: 14 residues processed: 88 average time/residue: 0.1740 time to fit residues: 24.3826 Evaluate side-chains 81 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 427 TRP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 428 GLN Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 87 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 270 optimal weight: 0.3980 chunk 229 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.034613 restraints weight = 170440.267| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.96 r_work: 0.2916 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 25658 Z= 0.111 Angle : 0.615 18.210 35046 Z= 0.287 Chirality : 0.045 0.430 4173 Planarity : 0.004 0.150 4302 Dihedral : 5.083 71.509 3283 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.49 % Rotamer: Outliers : 0.94 % Allowed : 9.93 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.19 (0.16), residues: 2991 helix: 1.17 (0.26), residues: 444 sheet: -0.01 (0.16), residues: 1044 loop : 0.04 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 113 TYR 0.012 0.001 TYR R 33 PHE 0.008 0.001 PHE F 144 TRP 0.027 0.001 TRP B 427 HIS 0.002 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (25519) covalent geometry : angle 0.56483 / 0.28 (34674) SS BOND : bond 0.00200 / 0.12 ( 45) SS BOND : angle 0.46678 / 0.32 ( 90) hydrogen bonds : bond 0.03793 / 2.64 ( 706) hydrogen bonds : angle 4.94534 / 3.40 ( 1884) link_ALPHA1-2 : bond 0.00550 / 0.28 ( 9) link_ALPHA1-2 : angle 2.67176 / 1.55 ( 27) link_ALPHA1-3 : bond 0.01001 / 0.54 ( 7) link_ALPHA1-3 : angle 1.71688 / 1.02 ( 21) link_ALPHA1-6 : bond 0.00620 / 0.31 ( 7) link_ALPHA1-6 : angle 1.55940 / 0.94 ( 21) link_BETA1-4 : bond 0.01569 / 0.88 ( 24) link_BETA1-4 : angle 4.17683 / 3.11 ( 72) link_NAG-ASN : bond 0.00262 / 0.19 ( 47) link_NAG-ASN : angle 2.08292 / 1.44 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 1.101 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: M 4 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7323 (tpp) REVERT: M 42 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: M 174 LYS cc_start: 0.8601 (pttm) cc_final: 0.8253 (pptt) REVERT: S 584 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8300 (mt-10) REVERT: W 475 MET cc_start: 0.8013 (mtt) cc_final: 0.7718 (mtp) REVERT: B 475 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6940 (mpp) REVERT: F 4 MET cc_start: 0.7973 (mmm) cc_final: 0.7638 (tpp) REVERT: F 79 LYS cc_start: 0.9414 (tttt) cc_final: 0.9175 (mtmm) REVERT: F 174 LYS cc_start: 0.8223 (pttm) cc_final: 0.7469 (mppt) REVERT: H 519 PHE cc_start: 0.6051 (t80) cc_final: 0.5532 (t80) REVERT: J 95 MET cc_start: 0.8705 (ptm) cc_final: 0.8273 (ttp) REVERT: J 97 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8976 (mtmm) REVERT: J 150 MET cc_start: 0.4801 (tpt) cc_final: 0.4217 (tpt) REVERT: O 4 MET cc_start: 0.7831 (mmt) cc_final: 0.7271 (mmt) REVERT: O 131 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8168 (pptt) REVERT: Q 519 PHE cc_start: 0.6326 (t80) cc_final: 0.6076 (t80) REVERT: Q 584 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8381 (mt-10) outliers start: 25 outliers final: 10 residues processed: 90 average time/residue: 0.1709 time to fit residues: 24.6161 Evaluate side-chains 83 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 428 GLN Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 8.9990 chunk 164 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 242 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 158 optimal weight: 40.0000 chunk 64 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 chunk 193 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.047780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033559 restraints weight = 170173.879| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.95 r_work: 0.2873 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25658 Z= 0.224 Angle : 0.687 18.277 35046 Z= 0.321 Chirality : 0.047 0.454 4173 Planarity : 0.005 0.153 4302 Dihedral : 5.235 73.885 3282 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.09 % Allowed : 9.89 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.00 (0.16), residues: 2991 helix: 1.00 (0.26), residues: 444 sheet: -0.16 (0.16), residues: 1050 loop : -0.05 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 147 TYR 0.017 0.002 TYR R 33 PHE 0.015 0.002 PHE F 103 TRP 0.030 0.002 TRP W 427 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (25519) covalent geometry : angle 0.63829 / 0.31 (34674) SS BOND : bond 0.00318 / 0.19 ( 45) SS BOND : angle 0.68042 / 0.47 ( 90) hydrogen bonds : bond 0.04489 / 3.09 ( 706) hydrogen bonds : angle 5.11494 / 3.52 ( 1884) link_ALPHA1-2 : bond 0.00170 / 0.10 ( 9) link_ALPHA1-2 : angle 3.01904 / 1.76 ( 27) link_ALPHA1-3 : bond 0.01024 / 0.51 ( 7) link_ALPHA1-3 : angle 1.78765 / 1.07 ( 21) link_ALPHA1-6 : bond 0.00471 / 0.23 ( 7) link_ALPHA1-6 : angle 1.68783 / 1.02 ( 21) link_BETA1-4 : bond 0.01519 / 0.85 ( 24) link_BETA1-4 : angle 4.28999 / 3.17 ( 72) link_NAG-ASN : bond 0.00386 / 0.26 ( 47) link_NAG-ASN : angle 2.22195 / 1.51 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: S 584 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8450 (mt-10) REVERT: W 475 MET cc_start: 0.7853 (mtt) cc_final: 0.7563 (mtp) REVERT: B 475 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6111 (mpp) REVERT: F 4 MET cc_start: 0.8008 (mmm) cc_final: 0.7772 (mmm) REVERT: F 79 LYS cc_start: 0.9423 (tttt) cc_final: 0.9140 (mtmm) REVERT: F 174 LYS cc_start: 0.8247 (pttm) cc_final: 0.7534 (mppt) REVERT: H 519 PHE cc_start: 0.5787 (t80) cc_final: 0.5384 (t80) REVERT: J 95 MET cc_start: 0.8740 (ptm) cc_final: 0.8228 (ttp) REVERT: J 150 MET cc_start: 0.4843 (tpt) cc_final: 0.4245 (tpt) REVERT: O 4 MET cc_start: 0.8018 (mmt) cc_final: 0.7733 (mmm) REVERT: Q 519 PHE cc_start: 0.6442 (t80) cc_final: 0.6165 (t80) REVERT: Q 530 MET cc_start: 0.7722 (mtt) cc_final: 0.7490 (mtt) REVERT: Q 584 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8414 (mt-10) outliers start: 29 outliers final: 16 residues processed: 89 average time/residue: 0.1663 time to fit residues: 24.0643 Evaluate side-chains 84 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 427 TRP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain H residue 630 GLN Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 169 optimal weight: 0.3980 chunk 35 optimal weight: 30.0000 chunk 285 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN O 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.047915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.033927 restraints weight = 168185.601| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.85 r_work: 0.2886 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25658 Z= 0.172 Angle : 0.649 18.248 35046 Z= 0.303 Chirality : 0.046 0.448 4173 Planarity : 0.005 0.151 4302 Dihedral : 5.158 72.878 3282 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 0.86 % Allowed : 10.15 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.02 (0.16), residues: 2991 helix: 1.08 (0.26), residues: 444 sheet: -0.16 (0.16), residues: 1050 loop : -0.05 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 113 TYR 0.014 0.001 TYR R 33 PHE 0.012 0.001 PHE J 93 TRP 0.029 0.002 TRP W 427 HIS 0.004 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (25519) covalent geometry : angle 0.59945 / 0.29 (34674) SS BOND : bond 0.00261 / 0.16 ( 45) SS BOND : angle 0.55082 / 0.38 ( 90) hydrogen bonds : bond 0.04213 / 2.91 ( 706) hydrogen bonds : angle 5.00156 / 3.44 ( 1884) link_ALPHA1-2 : bond 0.00251 / 0.13 ( 9) link_ALPHA1-2 : angle 2.90136 / 1.69 ( 27) link_ALPHA1-3 : bond 0.00970 / 0.50 ( 7) link_ALPHA1-3 : angle 1.75119 / 1.04 ( 21) link_ALPHA1-6 : bond 0.00543 / 0.26 ( 7) link_ALPHA1-6 : angle 1.67502 / 1.01 ( 21) link_BETA1-4 : bond 0.01536 / 0.85 ( 24) link_BETA1-4 : angle 4.22086 / 3.14 ( 72) link_NAG-ASN : bond 0.00286 / 0.20 ( 47) link_NAG-ASN : angle 2.12296 / 1.45 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8934 (tt0) REVERT: S 584 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8447 (mt-10) REVERT: W 475 MET cc_start: 0.7893 (mtt) cc_final: 0.7631 (mtp) REVERT: F 79 LYS cc_start: 0.9401 (tttt) cc_final: 0.9151 (mtmm) REVERT: F 174 LYS cc_start: 0.8238 (pttm) cc_final: 0.7538 (mppt) REVERT: H 519 PHE cc_start: 0.6153 (t80) cc_final: 0.5651 (t80) REVERT: J 150 MET cc_start: 0.5123 (tpt) cc_final: 0.4537 (tpt) REVERT: O 4 MET cc_start: 0.7980 (mmt) cc_final: 0.7268 (mmt) REVERT: Q 519 PHE cc_start: 0.6334 (t80) cc_final: 0.6051 (t80) REVERT: Q 530 MET cc_start: 0.7876 (mtt) cc_final: 0.7615 (mtt) REVERT: Q 584 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8408 (mt-10) outliers start: 23 outliers final: 14 residues processed: 84 average time/residue: 0.1605 time to fit residues: 22.2371 Evaluate side-chains 81 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 427 TRP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain H residue 630 GLN Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 287 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 238 optimal weight: 0.0030 chunk 219 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.048626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.034511 restraints weight = 170915.636| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.03 r_work: 0.2909 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 25658 Z= 0.099 Angle : 0.591 18.182 35046 Z= 0.275 Chirality : 0.044 0.426 4173 Planarity : 0.004 0.145 4302 Dihedral : 4.807 71.969 3282 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 0.64 % Allowed : 10.34 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.23 (0.16), residues: 2991 helix: 1.36 (0.26), residues: 447 sheet: -0.01 (0.16), residues: 1050 loop : 0.04 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 113 TYR 0.011 0.001 TYR N 33 PHE 0.019 0.001 PHE S 519 TRP 0.030 0.001 TRP W 427 HIS 0.002 0.000 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (25519) covalent geometry : angle 0.54339 / 0.26 (34674) SS BOND : bond 0.00187 / 0.12 ( 45) SS BOND : angle 0.43464 / 0.29 ( 90) hydrogen bonds : bond 0.03389 / 2.36 ( 706) hydrogen bonds : angle 4.68030 / 3.22 ( 1884) link_ALPHA1-2 : bond 0.00664 / 0.35 ( 9) link_ALPHA1-2 : angle 2.63215 / 1.52 ( 27) link_ALPHA1-3 : bond 0.01025 / 0.58 ( 7) link_ALPHA1-3 : angle 1.55592 / 0.91 ( 21) link_ALPHA1-6 : bond 0.00665 / 0.33 ( 7) link_ALPHA1-6 : angle 1.53199 / 0.92 ( 21) link_BETA1-4 : bond 0.01552 / 0.88 ( 24) link_BETA1-4 : angle 4.08199 / 3.05 ( 72) link_NAG-ASN : bond 0.00323 / 0.23 ( 47) link_NAG-ASN : angle 1.90506 / 1.33 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: M 174 LYS cc_start: 0.8581 (pttm) cc_final: 0.7710 (mppt) REVERT: R 78 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (p) REVERT: S 584 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8264 (mt-10) REVERT: W 475 MET cc_start: 0.7903 (mtt) cc_final: 0.7611 (mtp) REVERT: F 79 LYS cc_start: 0.9483 (tttt) cc_final: 0.9148 (mtmm) REVERT: F 174 LYS cc_start: 0.8186 (pttm) cc_final: 0.7502 (mppt) REVERT: H 519 PHE cc_start: 0.6123 (t80) cc_final: 0.5753 (t80) REVERT: J 150 MET cc_start: 0.5139 (tpt) cc_final: 0.4593 (tpt) REVERT: O 4 MET cc_start: 0.7793 (mmt) cc_final: 0.7153 (mmt) REVERT: Q 519 PHE cc_start: 0.6455 (t80) cc_final: 0.5904 (t80) REVERT: Q 530 MET cc_start: 0.7751 (mtt) cc_final: 0.7547 (mtt) REVERT: Q 584 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8310 (mt-10) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.1676 time to fit residues: 23.1541 Evaluate side-chains 79 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain S residue 630 GLN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 116 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 123 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.048068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.033939 restraints weight = 170830.930| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.95 r_work: 0.2883 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25658 Z= 0.148 Angle : 0.650 36.822 35046 Z= 0.290 Chirality : 0.045 0.433 4173 Planarity : 0.005 0.227 4302 Dihedral : 4.827 73.564 3281 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 0.56 % Allowed : 10.64 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.18 (0.16), residues: 2991 helix: 1.38 (0.27), residues: 447 sheet: -0.07 (0.16), residues: 1062 loop : -0.00 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 113 TYR 0.017 0.001 TYR N 33 PHE 0.010 0.001 PHE B 53 TRP 0.032 0.001 TRP W 427 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (25519) covalent geometry : angle 0.60495 / 0.28 (34674) SS BOND : bond 0.00254 / 0.15 ( 45) SS BOND : angle 0.67637 / 0.50 ( 90) hydrogen bonds : bond 0.03709 / 2.57 ( 706) hydrogen bonds : angle 4.73307 / 3.25 ( 1884) link_ALPHA1-2 : bond 0.00269 / 0.13 ( 9) link_ALPHA1-2 : angle 2.82883 / 1.64 ( 27) link_ALPHA1-3 : bond 0.00931 / 0.49 ( 7) link_ALPHA1-3 : angle 1.59275 / 0.94 ( 21) link_ALPHA1-6 : bond 0.00510 / 0.25 ( 7) link_ALPHA1-6 : angle 1.59702 / 0.96 ( 21) link_BETA1-4 : bond 0.01551 / 0.86 ( 24) link_BETA1-4 : angle 4.12650 / 3.07 ( 72) link_NAG-ASN : bond 0.00264 / 0.19 ( 47) link_NAG-ASN : angle 1.95777 / 1.35 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: M 174 LYS cc_start: 0.8531 (pttm) cc_final: 0.7649 (mppt) REVERT: S 584 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8408 (mt-10) REVERT: W 475 MET cc_start: 0.7942 (mtt) cc_final: 0.7659 (mtp) REVERT: F 79 LYS cc_start: 0.9423 (tttt) cc_final: 0.9134 (mtmm) REVERT: F 174 LYS cc_start: 0.8171 (pttm) cc_final: 0.7490 (mppt) REVERT: H 519 PHE cc_start: 0.6110 (t80) cc_final: 0.5699 (t80) REVERT: J 150 MET cc_start: 0.5250 (tpt) cc_final: 0.4687 (tpt) REVERT: O 4 MET cc_start: 0.7927 (mmt) cc_final: 0.7188 (mmt) REVERT: Q 519 PHE cc_start: 0.6351 (t80) cc_final: 0.6134 (t80) REVERT: Q 530 MET cc_start: 0.7874 (mtt) cc_final: 0.7612 (mtt) REVERT: Q 584 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8370 (mt-10) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1861 time to fit residues: 24.1249 Evaluate side-chains 78 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain S residue 630 GLN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 427 TRP Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 414 ILE Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 286 optimal weight: 0.6980 chunk 291 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.048293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034129 restraints weight = 170399.954| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.02 r_work: 0.2890 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25658 Z= 0.118 Angle : 0.624 29.215 35046 Z= 0.281 Chirality : 0.044 0.429 4173 Planarity : 0.005 0.205 4302 Dihedral : 4.774 74.150 3281 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 0.60 % Allowed : 10.71 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 0.23 (0.16), residues: 2991 helix: 1.44 (0.27), residues: 447 sheet: -0.04 (0.16), residues: 1050 loop : 0.04 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 113 TYR 0.014 0.001 TYR N 33 PHE 0.021 0.001 PHE S 519 TRP 0.031 0.001 TRP W 427 HIS 0.002 0.001 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25519) covalent geometry : angle 0.57864 / 0.27 (34674) SS BOND : bond 0.00212 / 0.13 ( 45) SS BOND : angle 0.57860 / 0.43 ( 90) hydrogen bonds : bond 0.03556 / 2.46 ( 706) hydrogen bonds : angle 4.66688 / 3.21 ( 1884) link_ALPHA1-2 : bond 0.00392 / 0.20 ( 9) link_ALPHA1-2 : angle 2.77650 / 1.60 ( 27) link_ALPHA1-3 : bond 0.00921 / 0.50 ( 7) link_ALPHA1-3 : angle 1.58517 / 0.93 ( 21) link_ALPHA1-6 : bond 0.00582 / 0.29 ( 7) link_ALPHA1-6 : angle 1.57703 / 0.95 ( 21) link_BETA1-4 : bond 0.01545 / 0.86 ( 24) link_BETA1-4 : angle 4.06586 / 3.03 ( 72) link_NAG-ASN : bond 0.00240 / 0.18 ( 47) link_NAG-ASN : angle 1.90298 / 1.32 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5170.51 seconds wall clock time: 89 minutes 50.97 seconds (5390.97 seconds total)