Starting phenix.real_space_refine on Sat Jun 21 18:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_27628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_27628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_27628.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_27628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp1_27628/06_2025/8dp1_27628.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 30 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 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 dihedrals: 30 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 9 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 dihedrals: 24 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 dihedrals: 24 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 dihedrals: 9 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 dihedrals: 24 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.29, per 1000 atoms: 0.61 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: 6.86 Conformation dependent library (CDL) restraints added in 3.0 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: 3.19 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: 9.22 Time building geometry restraints manager: 8.06 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 - 22.83: 15596 22.83 - 45.65: 684 45.65 - 68.48: 142 68.48 - 91.30: 89 91.30 - 114.13: 36 Dihedral angle restraints: 16547 sinusoidal: 7766 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 16544 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 57.360 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.170 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 15.881 114.125 10760 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (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 TRP 0.237 0.029 TRP N 47 HIS 0.024 0.005 HIS N 111 PHE 0.083 0.014 PHE J 383 TYR 0.201 0.025 TYR E 206 ARG 0.012 0.001 ARG R 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00980 ( 47) link_NAG-ASN : angle 4.53875 ( 141) link_ALPHA1-6 : bond 0.02556 ( 7) link_ALPHA1-6 : angle 6.51533 ( 21) link_BETA1-4 : bond 0.02525 ( 24) link_BETA1-4 : angle 6.45995 ( 72) link_ALPHA1-2 : bond 0.01056 ( 9) link_ALPHA1-2 : angle 4.25947 ( 27) link_ALPHA1-3 : bond 0.02524 ( 7) link_ALPHA1-3 : angle 6.04465 ( 21) hydrogen bonds : bond 0.17152 ( 706) hydrogen bonds : angle 8.25201 ( 1884) SS BOND : bond 0.00594 ( 45) SS BOND : angle 2.04820 ( 90) covalent geometry : bond 0.01395 (25519) covalent geometry : angle 1.84797 (34674) *********************** 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 : 3.182 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: 0.5564 time to fit residues: 142.4855 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 : 2.745 ------------------------------------------------------------------------------- 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 253 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 616 ASN W 448 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 = 0.3626 r_free = 0.3626 target = 0.049763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.035675 restraints weight = 170927.687| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.98 r_work: 0.2959 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 25658 Z= 0.152 Angle : 0.785 19.730 35046 Z= 0.376 Chirality : 0.048 0.408 4173 Planarity : 0.005 0.163 4302 Dihedral : 11.879 95.121 5225 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 1.20 % Allowed : 6.63 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2991 helix: 0.35 (0.25), residues: 426 sheet: -0.08 (0.15), residues: 1050 loop : 0.03 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP W 427 HIS 0.005 0.001 HIS J 66 PHE 0.012 0.002 PHE R 178 TYR 0.014 0.001 TYR R 206 ARG 0.007 0.001 ARG F 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 47) link_NAG-ASN : angle 2.74875 ( 141) link_ALPHA1-6 : bond 0.00742 ( 7) link_ALPHA1-6 : angle 1.87764 ( 21) link_BETA1-4 : bond 0.01682 ( 24) link_BETA1-4 : angle 5.00596 ( 72) link_ALPHA1-2 : bond 0.00627 ( 9) link_ALPHA1-2 : angle 2.87139 ( 27) link_ALPHA1-3 : bond 0.01182 ( 7) link_ALPHA1-3 : angle 2.54897 ( 21) hydrogen bonds : bond 0.05590 ( 706) hydrogen bonds : angle 5.95541 ( 1884) SS BOND : bond 0.00282 ( 45) SS BOND : angle 0.80212 ( 90) covalent geometry : bond 0.00324 (25519) covalent geometry : angle 0.72490 (34674) *********************** 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 123 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: M 174 LYS cc_start: 0.8641 (pttm) cc_final: 0.8326 (pptt) REVERT: S 519 PHE cc_start: 0.5537 (t80) cc_final: 0.5156 (t80) REVERT: S 584 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8331 (mt-10) REVERT: S 626 MET cc_start: 0.7941 (mtm) cc_final: 0.7594 (mtp) REVERT: W 475 MET cc_start: 0.8064 (mtt) cc_final: 0.7339 (mtt) REVERT: F 128 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5775 (p0) REVERT: F 147 ARG cc_start: 0.7132 (ttm-80) cc_final: 0.6815 (tpt170) REVERT: J 475 MET cc_start: 0.8294 (mtt) cc_final: 0.8088 (mmt) REVERT: O 42 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8813 (tt0) REVERT: O 131 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8121 (pttm) REVERT: Q 519 PHE cc_start: 0.6537 (t80) cc_final: 0.6300 (t80) REVERT: Q 530 MET cc_start: 0.8518 (mtp) cc_final: 0.8260 (mtp) REVERT: Q 584 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8366 (mt-10) outliers start: 32 outliers final: 7 residues processed: 123 average time/residue: 0.4718 time to fit residues: 88.0080 Evaluate side-chains 80 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 2.955 ------------------------------------------------------------------------------- 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 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 428 GLN Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 42 GLN 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 95 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 279 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 432 GLN W 478 ASN J 428 GLN Q 577 GLN Q 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.048317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033913 restraints weight = 169375.996| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.02 r_work: 0.2889 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25658 Z= 0.233 Angle : 0.761 19.212 35046 Z= 0.363 Chirality : 0.049 0.430 4173 Planarity : 0.005 0.161 4302 Dihedral : 10.769 93.880 5212 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.16 % Allowed : 7.75 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2991 helix: 0.55 (0.26), residues: 426 sheet: -0.12 (0.15), residues: 1035 loop : -0.09 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP W 427 HIS 0.006 0.001 HIS J 105 PHE 0.014 0.002 PHE F 103 TYR 0.019 0.002 TYR R 33 ARG 0.012 0.001 ARG O 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 47) link_NAG-ASN : angle 2.62950 ( 141) link_ALPHA1-6 : bond 0.00743 ( 7) link_ALPHA1-6 : angle 1.87596 ( 21) link_BETA1-4 : bond 0.01641 ( 24) link_BETA1-4 : angle 4.88542 ( 72) link_ALPHA1-2 : bond 0.00351 ( 9) link_ALPHA1-2 : angle 3.23645 ( 27) link_ALPHA1-3 : bond 0.01442 ( 7) link_ALPHA1-3 : angle 1.73343 ( 21) hydrogen bonds : bond 0.05408 ( 706) hydrogen bonds : angle 5.69037 ( 1884) SS BOND : bond 0.00348 ( 45) SS BOND : angle 0.75380 ( 90) covalent geometry : bond 0.00543 (25519) covalent geometry : angle 0.70308 (34674) *********************** 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 100 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8929 (tt0) REVERT: M 174 LYS cc_start: 0.8691 (pttm) cc_final: 0.7800 (mppt) REVERT: S 519 PHE cc_start: 0.5580 (t80) cc_final: 0.5159 (t80) REVERT: S 584 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8433 (mt-10) REVERT: W 475 MET cc_start: 0.8028 (mtt) cc_final: 0.7579 (mtt) REVERT: F 147 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.6775 (tpt170) REVERT: F 174 LYS cc_start: 0.8279 (pttm) cc_final: 0.7393 (mppt) REVERT: H 519 PHE cc_start: 0.5786 (t80) cc_final: 0.5559 (t80) REVERT: O 4 MET cc_start: 0.7869 (mmt) cc_final: 0.7535 (mmt) REVERT: O 42 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8907 (tt0) REVERT: Q 519 PHE cc_start: 0.6551 (t80) cc_final: 0.6282 (t80) REVERT: Q 584 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8413 (mt-10) outliers start: 31 outliers final: 10 residues processed: 95 average time/residue: 0.4230 time to fit residues: 65.5435 Evaluate side-chains 77 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 3.150 ------------------------------------------------------------------------------- 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 B residue 286 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain H residue 635 ILE Chi-restraints excluded: chain J residue 108 ILE 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 O residue 42 GLN 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 119 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.047852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033625 restraints weight = 171793.754| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.94 r_work: 0.2870 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 25658 Z= 0.257 Angle : 0.748 19.188 35046 Z= 0.355 Chirality : 0.049 0.441 4173 Planarity : 0.005 0.161 4302 Dihedral : 10.291 94.128 5212 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.01 % Allowed : 8.73 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2991 helix: 0.59 (0.26), residues: 429 sheet: -0.32 (0.15), residues: 1059 loop : -0.11 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP W 427 HIS 0.004 0.001 HIS R 111 PHE 0.016 0.002 PHE J 468 TYR 0.018 0.002 TYR R 33 ARG 0.004 0.001 ARG O 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 47) link_NAG-ASN : angle 2.54019 ( 141) link_ALPHA1-6 : bond 0.00568 ( 7) link_ALPHA1-6 : angle 1.87450 ( 21) link_BETA1-4 : bond 0.01591 ( 24) link_BETA1-4 : angle 4.78235 ( 72) link_ALPHA1-2 : bond 0.00374 ( 9) link_ALPHA1-2 : angle 3.41728 ( 27) link_ALPHA1-3 : bond 0.01258 ( 7) link_ALPHA1-3 : angle 1.89572 ( 21) hydrogen bonds : bond 0.05164 ( 706) hydrogen bonds : angle 5.56416 ( 1884) SS BOND : bond 0.00354 ( 45) SS BOND : angle 0.71558 ( 90) covalent geometry : bond 0.00600 (25519) covalent geometry : angle 0.69023 (34674) *********************** 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 95 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: M 174 LYS cc_start: 0.8646 (pttm) cc_final: 0.8288 (pptt) REVERT: S 584 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8450 (mt-10) REVERT: F 147 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.6657 (tmt-80) REVERT: F 174 LYS cc_start: 0.8252 (pttm) cc_final: 0.7395 (mppt) REVERT: J 475 MET cc_start: 0.7946 (mtt) cc_final: 0.7674 (mtm) REVERT: O 4 MET cc_start: 0.7812 (mmt) cc_final: 0.7519 (mmt) REVERT: Q 519 PHE cc_start: 0.6452 (t80) cc_final: 0.6128 (t80) REVERT: Q 584 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8444 (mt-10) outliers start: 27 outliers final: 12 residues processed: 89 average time/residue: 0.3898 time to fit residues: 57.2899 Evaluate side-chains 79 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 W residue 199 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain H residue 635 ILE Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain N residue 119 VAL 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 209 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 261 optimal weight: 40.0000 chunk 198 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 257 optimal weight: 40.0000 chunk 165 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 577 GLN ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 428 GLN ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN O 31 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.048048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.033789 restraints weight = 171923.223| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.98 r_work: 0.2881 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25658 Z= 0.204 Angle : 0.685 19.203 35046 Z= 0.324 Chirality : 0.047 0.443 4173 Planarity : 0.005 0.159 4302 Dihedral : 9.760 89.015 5212 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 0.97 % Allowed : 9.70 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2991 helix: 0.80 (0.26), residues: 444 sheet: -0.30 (0.15), residues: 1056 loop : -0.11 (0.17), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP W 427 HIS 0.005 0.001 HIS B 105 PHE 0.012 0.002 PHE W 468 TYR 0.016 0.001 TYR R 33 ARG 0.003 0.000 ARG W 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 47) link_NAG-ASN : angle 2.32774 ( 141) link_ALPHA1-6 : bond 0.00683 ( 7) link_ALPHA1-6 : angle 1.84271 ( 21) link_BETA1-4 : bond 0.01585 ( 24) link_BETA1-4 : angle 4.61050 ( 72) link_ALPHA1-2 : bond 0.00281 ( 9) link_ALPHA1-2 : angle 3.35718 ( 27) link_ALPHA1-3 : bond 0.01309 ( 7) link_ALPHA1-3 : angle 1.73331 ( 21) hydrogen bonds : bond 0.04627 ( 706) hydrogen bonds : angle 5.33141 ( 1884) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.62862 ( 90) covalent geometry : bond 0.00473 (25519) covalent geometry : angle 0.62806 (34674) *********************** 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 92 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8940 (tt0) REVERT: M 174 LYS cc_start: 0.8657 (pttm) cc_final: 0.8315 (pptt) REVERT: S 584 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8438 (mt-10) REVERT: F 147 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.6651 (tmt-80) REVERT: F 174 LYS cc_start: 0.8264 (pttm) cc_final: 0.7478 (mppt) REVERT: J 150 MET cc_start: 0.4271 (tpt) cc_final: 0.3549 (tpt) REVERT: O 4 MET cc_start: 0.7891 (mmt) cc_final: 0.7305 (mmt) REVERT: Q 519 PHE cc_start: 0.6390 (t80) cc_final: 0.6078 (t80) REVERT: Q 584 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8412 (mt-10) outliers start: 26 outliers final: 14 residues processed: 88 average time/residue: 0.4007 time to fit residues: 57.9992 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 : 2.796 ------------------------------------------------------------------------------- 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 427 TRP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 428 GLN Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain H residue 635 ILE Chi-restraints excluded: chain J residue 108 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 287 optimal weight: 0.0060 chunk 108 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 243 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3579 r_free = 0.3579 target = 0.048365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.034212 restraints weight = 169755.339| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.98 r_work: 0.2898 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25658 Z= 0.130 Angle : 0.632 18.928 35046 Z= 0.297 Chirality : 0.045 0.426 4173 Planarity : 0.004 0.154 4302 Dihedral : 9.236 81.103 5212 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 1.20 % Allowed : 9.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2991 helix: 1.00 (0.26), residues: 444 sheet: -0.17 (0.15), residues: 1050 loop : -0.05 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP W 427 HIS 0.003 0.001 HIS E 111 PHE 0.009 0.001 PHE J 468 TYR 0.013 0.001 TYR R 33 ARG 0.005 0.000 ARG B 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 47) link_NAG-ASN : angle 2.18028 ( 141) link_ALPHA1-6 : bond 0.00746 ( 7) link_ALPHA1-6 : angle 1.74223 ( 21) link_BETA1-4 : bond 0.01629 ( 24) link_BETA1-4 : angle 4.47728 ( 72) link_ALPHA1-2 : bond 0.00363 ( 9) link_ALPHA1-2 : angle 3.23284 ( 27) link_ALPHA1-3 : bond 0.01275 ( 7) link_ALPHA1-3 : angle 1.67950 ( 21) hydrogen bonds : bond 0.04104 ( 706) hydrogen bonds : angle 5.09614 ( 1884) SS BOND : bond 0.00241 ( 45) SS BOND : angle 0.51296 ( 90) covalent geometry : bond 0.00289 (25519) covalent geometry : angle 0.57433 (34674) *********************** 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 99 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 4 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7365 (tpp) REVERT: M 42 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: M 174 LYS cc_start: 0.8612 (pttm) cc_final: 0.8261 (pptt) REVERT: S 584 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8335 (mt-10) REVERT: F 79 LYS cc_start: 0.9374 (tttt) cc_final: 0.9150 (mtmm) REVERT: F 147 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6797 (tpt170) REVERT: F 174 LYS cc_start: 0.8227 (pttm) cc_final: 0.7437 (mppt) REVERT: J 97 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (mtmm) REVERT: J 150 MET cc_start: 0.4364 (tpt) cc_final: 0.3663 (tpt) REVERT: O 4 MET cc_start: 0.7805 (mmt) cc_final: 0.7243 (mmt) REVERT: Q 519 PHE cc_start: 0.6358 (t80) cc_final: 0.6093 (t80) REVERT: Q 530 MET cc_start: 0.8181 (mtp) cc_final: 0.7950 (mtt) REVERT: Q 584 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8422 (mt-10) outliers start: 32 outliers final: 14 residues processed: 94 average time/residue: 0.4246 time to fit residues: 63.7267 Evaluate side-chains 83 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 3.024 ------------------------------------------------------------------------------- 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 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 B residue 134 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain J residue 97 LYS Chi-restraints excluded: chain J residue 108 ILE 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 57 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 172 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.048389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.034388 restraints weight = 169555.246| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.91 r_work: 0.2906 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25658 Z= 0.129 Angle : 0.614 18.824 35046 Z= 0.287 Chirality : 0.045 0.419 4173 Planarity : 0.004 0.151 4302 Dihedral : 8.778 74.090 5212 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 10.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2991 helix: 1.16 (0.26), residues: 444 sheet: -0.10 (0.16), residues: 1050 loop : -0.02 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP W 427 HIS 0.003 0.001 HIS E 111 PHE 0.016 0.001 PHE S 519 TYR 0.013 0.001 TYR R 33 ARG 0.004 0.000 ARG M 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 47) link_NAG-ASN : angle 2.08234 ( 141) link_ALPHA1-6 : bond 0.00722 ( 7) link_ALPHA1-6 : angle 1.70386 ( 21) link_BETA1-4 : bond 0.01615 ( 24) link_BETA1-4 : angle 4.41116 ( 72) link_ALPHA1-2 : bond 0.00325 ( 9) link_ALPHA1-2 : angle 3.22974 ( 27) link_ALPHA1-3 : bond 0.01247 ( 7) link_ALPHA1-3 : angle 1.57481 ( 21) hydrogen bonds : bond 0.03824 ( 706) hydrogen bonds : angle 4.91255 ( 1884) SS BOND : bond 0.00245 ( 45) SS BOND : angle 0.49752 ( 90) covalent geometry : bond 0.00291 (25519) covalent geometry : angle 0.55807 (34674) *********************** 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 92 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 4 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7457 (tpp) REVERT: M 42 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8899 (tt0) REVERT: M 174 LYS cc_start: 0.8600 (pttm) cc_final: 0.7670 (mppt) REVERT: S 584 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 327 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8206 (mtm180) REVERT: B 428 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6126 (mp10) REVERT: F 79 LYS cc_start: 0.9375 (tttt) cc_final: 0.9147 (mtmm) REVERT: F 174 LYS cc_start: 0.8192 (pttm) cc_final: 0.7425 (mppt) REVERT: J 95 MET cc_start: 0.8558 (ptm) cc_final: 0.7959 (ttp) REVERT: J 150 MET cc_start: 0.4866 (tpt) cc_final: 0.4303 (tpt) REVERT: O 4 MET cc_start: 0.7861 (mmt) cc_final: 0.7324 (mmt) REVERT: Q 519 PHE cc_start: 0.6283 (t80) cc_final: 0.6015 (t80) REVERT: Q 584 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8395 (mt-10) outliers start: 24 outliers final: 15 residues processed: 86 average time/residue: 0.4251 time to fit residues: 58.6270 Evaluate side-chains 86 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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 S residue 616 ASN Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 428 GLN Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain H residue 626 MET 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 221 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 283 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 262 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.047944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.033902 restraints weight = 169482.314| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.87 r_work: 0.2885 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3451 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= 0.193 Angle : 0.654 18.940 35046 Z= 0.306 Chirality : 0.046 0.427 4173 Planarity : 0.005 0.151 4302 Dihedral : 8.881 75.055 5212 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.16 % Allowed : 10.30 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2991 helix: 1.11 (0.26), residues: 444 sheet: -0.17 (0.16), residues: 1050 loop : -0.06 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 427 HIS 0.004 0.001 HIS E 111 PHE 0.012 0.002 PHE O 103 TYR 0.015 0.001 TYR R 33 ARG 0.004 0.000 ARG M 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 47) link_NAG-ASN : angle 2.16696 ( 141) link_ALPHA1-6 : bond 0.00629 ( 7) link_ALPHA1-6 : angle 1.74678 ( 21) link_BETA1-4 : bond 0.01585 ( 24) link_BETA1-4 : angle 4.45988 ( 72) link_ALPHA1-2 : bond 0.00197 ( 9) link_ALPHA1-2 : angle 3.36517 ( 27) link_ALPHA1-3 : bond 0.01243 ( 7) link_ALPHA1-3 : angle 1.61393 ( 21) hydrogen bonds : bond 0.04167 ( 706) hydrogen bonds : angle 4.98345 ( 1884) SS BOND : bond 0.00275 ( 45) SS BOND : angle 0.62810 ( 90) covalent geometry : bond 0.00446 (25519) covalent geometry : angle 0.59935 (34674) *********************** 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 96 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 4 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7439 (tpp) REVERT: M 42 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: S 584 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 327 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7413 (mtp180) REVERT: F 79 LYS cc_start: 0.9388 (tttt) cc_final: 0.9148 (mtmm) REVERT: F 174 LYS cc_start: 0.8203 (pttm) cc_final: 0.7421 (mppt) REVERT: J 95 MET cc_start: 0.8711 (ptm) cc_final: 0.8051 (ttp) REVERT: J 150 MET cc_start: 0.4914 (tpt) cc_final: 0.4356 (tpt) REVERT: J 475 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7371 (mpp) REVERT: O 4 MET cc_start: 0.7909 (mmt) cc_final: 0.7310 (mmt) REVERT: Q 519 PHE cc_start: 0.6309 (t80) cc_final: 0.6031 (t80) REVERT: Q 584 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8419 (mt-10) outliers start: 31 outliers final: 17 residues processed: 89 average time/residue: 0.3914 time to fit residues: 57.0278 Evaluate side-chains 86 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 199 SER 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 327 ARG Chi-restraints excluded: chain F residue 154 LYS 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 J residue 475 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 222 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 273 optimal weight: 30.0000 chunk 210 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 198 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.048703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.034822 restraints weight = 168943.990| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.86 r_work: 0.2896 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 25658 Z= 0.104 Angle : 0.602 18.819 35046 Z= 0.280 Chirality : 0.045 0.408 4173 Planarity : 0.004 0.146 4302 Dihedral : 8.213 72.098 5212 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 0.64 % Allowed : 10.64 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2991 helix: 1.33 (0.26), residues: 447 sheet: -0.06 (0.16), residues: 1050 loop : 0.01 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 427 HIS 0.009 0.001 HIS W 105 PHE 0.021 0.001 PHE S 519 TYR 0.018 0.001 TYR M 145 ARG 0.007 0.000 ARG M 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 47) link_NAG-ASN : angle 1.97057 ( 141) link_ALPHA1-6 : bond 0.00799 ( 7) link_ALPHA1-6 : angle 1.66276 ( 21) link_BETA1-4 : bond 0.01641 ( 24) link_BETA1-4 : angle 4.32682 ( 72) link_ALPHA1-2 : bond 0.00549 ( 9) link_ALPHA1-2 : angle 3.16784 ( 27) link_ALPHA1-3 : bond 0.01285 ( 7) link_ALPHA1-3 : angle 1.45435 ( 21) hydrogen bonds : bond 0.03508 ( 706) hydrogen bonds : angle 4.73572 ( 1884) SS BOND : bond 0.00193 ( 45) SS BOND : angle 0.42427 ( 90) covalent geometry : bond 0.00220 (25519) covalent geometry : angle 0.54850 (34674) *********************** 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 83 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8889 (tt0) REVERT: M 174 LYS cc_start: 0.8544 (pttm) cc_final: 0.7670 (mppt) REVERT: S 584 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8440 (mt-10) REVERT: B 327 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8160 (mtm180) REVERT: F 79 LYS cc_start: 0.9422 (tttt) cc_final: 0.9166 (mtmm) REVERT: F 174 LYS cc_start: 0.8196 (pttm) cc_final: 0.7440 (mppt) REVERT: J 150 MET cc_start: 0.5247 (tpt) cc_final: 0.4720 (tpt) REVERT: J 475 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7368 (mpp) REVERT: O 4 MET cc_start: 0.7861 (mmt) cc_final: 0.7349 (mmt) REVERT: Q 519 PHE cc_start: 0.6292 (t80) cc_final: 0.5813 (t80) REVERT: Q 530 MET cc_start: 0.7862 (mtp) cc_final: 0.7640 (mtt) REVERT: Q 584 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8439 (mt-10) outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 0.3889 time to fit residues: 50.7410 Evaluate side-chains 78 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain S residue 626 MET Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain F residue 154 LYS 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 J residue 475 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 210 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 187 optimal weight: 0.0470 chunk 173 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.048204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034143 restraints weight = 169777.014| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.93 r_work: 0.2893 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25658 Z= 0.159 Angle : 0.629 18.891 35046 Z= 0.292 Chirality : 0.045 0.421 4173 Planarity : 0.005 0.146 4302 Dihedral : 8.190 73.538 5211 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 0.67 % Allowed : 10.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2991 helix: 1.30 (0.27), residues: 447 sheet: -0.13 (0.16), residues: 1062 loop : -0.04 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP W 427 HIS 0.003 0.001 HIS R 212 PHE 0.009 0.001 PHE J 317 TYR 0.018 0.001 TYR N 33 ARG 0.007 0.000 ARG M 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 47) link_NAG-ASN : angle 2.05040 ( 141) link_ALPHA1-6 : bond 0.00655 ( 7) link_ALPHA1-6 : angle 1.70362 ( 21) link_BETA1-4 : bond 0.01603 ( 24) link_BETA1-4 : angle 4.35944 ( 72) link_ALPHA1-2 : bond 0.00174 ( 9) link_ALPHA1-2 : angle 3.32478 ( 27) link_ALPHA1-3 : bond 0.01222 ( 7) link_ALPHA1-3 : angle 1.56652 ( 21) hydrogen bonds : bond 0.03884 ( 706) hydrogen bonds : angle 4.80642 ( 1884) SS BOND : bond 0.00255 ( 45) SS BOND : angle 0.55821 ( 90) covalent geometry : bond 0.00368 (25519) covalent geometry : angle 0.57465 (34674) ********************** 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: 18 poor density : 64 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8898 (tt0) REVERT: M 174 LYS cc_start: 0.8527 (pttm) cc_final: 0.7667 (mppt) REVERT: S 584 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 327 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: F 79 LYS cc_start: 0.9384 (tttt) cc_final: 0.9144 (mtmm) REVERT: F 174 LYS cc_start: 0.8195 (pttm) cc_final: 0.7442 (mppt) REVERT: J 150 MET cc_start: 0.5327 (tpt) cc_final: 0.4774 (tpt) REVERT: J 475 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7265 (mpp) REVERT: O 4 MET cc_start: 0.7925 (mmt) cc_final: 0.7264 (mmt) REVERT: Q 519 PHE cc_start: 0.6320 (t80) cc_final: 0.6095 (t80) REVERT: Q 584 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8413 (mt-10) outliers start: 18 outliers final: 12 residues processed: 77 average time/residue: 0.4881 time to fit residues: 63.3673 Evaluate side-chains 79 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 2.988 ------------------------------------------------------------------------------- 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 132 THR Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain F residue 154 LYS 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 J residue 475 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 296 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS ** M 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN W 105 HIS W 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.047944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.033805 restraints weight = 170232.834| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.95 r_work: 0.2881 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25658 Z= 0.194 Angle : 0.658 18.970 35046 Z= 0.307 Chirality : 0.046 0.435 4173 Planarity : 0.005 0.147 4302 Dihedral : 8.291 73.400 5211 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 0.75 % Allowed : 10.60 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2991 helix: 1.12 (0.26), residues: 450 sheet: -0.19 (0.16), residues: 1002 loop : -0.14 (0.17), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP W 427 HIS 0.003 0.001 HIS E 111 PHE 0.021 0.002 PHE S 519 TYR 0.018 0.001 TYR N 33 ARG 0.005 0.000 ARG M 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 47) link_NAG-ASN : angle 2.12506 ( 141) link_ALPHA1-6 : bond 0.00656 ( 7) link_ALPHA1-6 : angle 1.73631 ( 21) link_BETA1-4 : bond 0.01570 ( 24) link_BETA1-4 : angle 4.39704 ( 72) link_ALPHA1-2 : bond 0.00182 ( 9) link_ALPHA1-2 : angle 3.44022 ( 27) link_ALPHA1-3 : bond 0.01236 ( 7) link_ALPHA1-3 : angle 1.60893 ( 21) hydrogen bonds : bond 0.04217 ( 706) hydrogen bonds : angle 4.90198 ( 1884) SS BOND : bond 0.00270 ( 45) SS BOND : angle 0.59797 ( 90) covalent geometry : bond 0.00452 (25519) covalent geometry : angle 0.60515 (34674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13432.69 seconds wall clock time: 233 minutes 58.96 seconds (14038.96 seconds total)