Starting phenix.real_space_refine on Mon Feb 19 14:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_27628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_27628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_27628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_27628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp1_27628/02_2024/8dp1_27628.pdb" } 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 Residue "M PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.89, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 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: 10.02 Conformation dependent library (CDL) restraints added in 4.4 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: 2.61 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: 8.36 Time building geometry restraints manager: 10.71 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: 97.47 - 105.04: 508 105.04 - 112.61: 12371 112.61 - 120.17: 11386 120.17 - 127.74: 10129 127.74 - 135.31: 280 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 2.440 nonbonded pdb=" OD1 ASP O 175 " pdb=" OG1 THR O 177 " model vdw 2.539 2.440 nonbonded pdb=" OG SER M 126 " pdb=" OD1 ASP M 128 " model vdw 2.540 2.440 nonbonded pdb=" OG SER O 126 " pdb=" OD1 ASP O 128 " model vdw 2.540 2.440 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 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: 2.640 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: 8.190 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 62.470 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.310 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.790 ------------------------------------------------------------------------------- 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 25519 Z= 0.893 Angle : 1.848 16.953 34674 Z= 1.196 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 *********************** 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 fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 2.885 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: 0.5257 time to fit residues: 134.4833 Evaluate side-chains 86 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 3.099 ------------------------------------------------------------------------------- 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: 4.9990 chunk 126 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 448 ASN W 478 ASN B 448 ASN J 105 HIS J 428 GLN J 448 ASN O 143 ASN Q 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 25519 Z= 0.223 Angle : 0.716 11.355 34674 Z= 0.360 Chirality : 0.048 0.395 4173 Planarity : 0.005 0.164 4302 Dihedral : 11.763 90.571 5225 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.81 % Favored : 97.06 % Rotamer: Outliers : 1.20 % Allowed : 6.97 % Favored : 91.84 % 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: 0.27 (0.25), residues: 426 sheet: 0.02 (0.16), residues: 1029 loop : -0.03 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP W 427 HIS 0.004 0.001 HIS J 66 PHE 0.016 0.002 PHE R 178 TYR 0.017 0.002 TYR R 206 ARG 0.007 0.001 ARG H 588 *********************** 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 119 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: M 174 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7633 (mppt) REVERT: R 216 ASN cc_start: 0.7772 (m-40) cc_final: 0.7506 (t0) REVERT: S 519 PHE cc_start: 0.5449 (t80) cc_final: 0.5083 (t80) REVERT: S 584 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7392 (mt-10) REVERT: S 626 MET cc_start: 0.7635 (mtm) cc_final: 0.7166 (mtp) REVERT: F 42 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: F 147 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6824 (tpt170) REVERT: O 42 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: O 131 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8034 (pttm) REVERT: Q 519 PHE cc_start: 0.6406 (t80) cc_final: 0.6205 (t80) REVERT: Q 530 MET cc_start: 0.8381 (mtp) cc_final: 0.8158 (mtp) REVERT: Q 584 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7449 (mt-10) outliers start: 32 outliers final: 8 residues processed: 118 average time/residue: 0.4432 time to fit residues: 80.3692 Evaluate side-chains 80 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain F residue 42 GLN 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 616 ASN Chi-restraints excluded: chain Q residue 658 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 294 optimal weight: 8.9990 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 218 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 577 GLN S 618 ASN W 432 GLN Q 577 GLN Q 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 25519 Z= 0.371 Angle : 0.702 11.926 34674 Z= 0.351 Chirality : 0.049 0.400 4173 Planarity : 0.005 0.162 4302 Dihedral : 10.798 89.534 5216 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 1.69 % Allowed : 7.60 % Favored : 90.71 % 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: -0.14 (0.15), residues: 2991 helix: 0.46 (0.25), residues: 444 sheet: -0.12 (0.15), residues: 1035 loop : -0.10 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 427 HIS 0.004 0.001 HIS E 111 PHE 0.014 0.002 PHE F 103 TYR 0.018 0.002 TYR R 33 ARG 0.012 0.001 ARG O 28 *********************** 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 111 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 66 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: S 519 PHE cc_start: 0.5457 (t80) cc_final: 0.5065 (t80) REVERT: S 584 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7462 (mt-10) REVERT: F 147 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6840 (tpt170) REVERT: O 4 MET cc_start: 0.7536 (mmt) cc_final: 0.7329 (mmt) REVERT: O 42 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: Q 519 PHE cc_start: 0.6343 (t80) cc_final: 0.6093 (t80) REVERT: Q 584 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7625 (mt-10) outliers start: 45 outliers final: 16 residues processed: 102 average time/residue: 0.3868 time to fit residues: 64.2370 Evaluate side-chains 83 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 113 ARG Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 426 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain E residue 216 ASN 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 616 ASN 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 269 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25519 Z= 0.295 Angle : 0.634 11.931 34674 Z= 0.316 Chirality : 0.047 0.392 4173 Planarity : 0.005 0.158 4302 Dihedral : 9.957 84.820 5213 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.12 % Allowed : 8.95 % Favored : 89.93 % 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: -0.09 (0.16), residues: 2991 helix: 0.71 (0.26), residues: 444 sheet: -0.13 (0.15), residues: 1038 loop : -0.10 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 427 HIS 0.005 0.001 HIS W 105 PHE 0.012 0.002 PHE J 468 TYR 0.015 0.002 TYR R 33 ARG 0.005 0.000 ARG O 28 *********************** 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 98 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 68 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: S 519 PHE cc_start: 0.5509 (t80) cc_final: 0.5154 (t80) REVERT: S 584 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7492 (mt-10) REVERT: W 475 MET cc_start: 0.7367 (mtt) cc_final: 0.7154 (mtt) REVERT: F 4 MET cc_start: 0.7840 (mmm) cc_final: 0.7303 (mmm) REVERT: F 147 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.6885 (tpt170) REVERT: O 4 MET cc_start: 0.7465 (mmt) cc_final: 0.7204 (mmt) REVERT: O 42 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: O 131 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8033 (pptt) REVERT: Q 519 PHE cc_start: 0.6206 (t80) cc_final: 0.5949 (t80) REVERT: Q 584 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7613 (mt-10) outliers start: 30 outliers final: 17 residues processed: 91 average time/residue: 0.4410 time to fit residues: 66.4228 Evaluate side-chains 85 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 3.227 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 426 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain E residue 216 ASN 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 426 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain O residue 42 GLN Chi-restraints excluded: chain Q residue 616 ASN 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 241 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 0.0470 chunk 119 optimal weight: 0.9990 chunk 247 optimal weight: 0.0770 chunk 200 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 332 ASN B 428 GLN H 652 GLN N 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 25519 Z= 0.158 Angle : 0.560 11.265 34674 Z= 0.276 Chirality : 0.045 0.373 4173 Planarity : 0.004 0.153 4302 Dihedral : 8.898 80.116 5213 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 1.01 % Allowed : 9.51 % Favored : 89.48 % 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: 0.14 (0.16), residues: 2991 helix: 1.10 (0.26), residues: 444 sheet: 0.03 (0.15), residues: 1050 loop : -0.03 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 427 HIS 0.007 0.001 HIS B 105 PHE 0.008 0.001 PHE F 144 TYR 0.012 0.001 TYR R 33 ARG 0.003 0.000 ARG W 476 *********************** 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 95 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: S 519 PHE cc_start: 0.5768 (t80) cc_final: 0.5455 (t80) REVERT: S 584 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7406 (mt-10) REVERT: W 44 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8977 (m) REVERT: J 150 MET cc_start: 0.4094 (tpt) cc_final: 0.3462 (tpt) REVERT: O 131 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8153 (pptt) REVERT: Q 519 PHE cc_start: 0.6133 (t80) cc_final: 0.5911 (t80) REVERT: Q 584 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7530 (mt-10) outliers start: 27 outliers final: 13 residues processed: 92 average time/residue: 0.3919 time to fit residues: 57.3824 Evaluate side-chains 80 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 44 VAL Chi-restraints excluded: chain W residue 286 VAL 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 Q residue 616 ASN 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 97 optimal weight: 8.9990 chunk 261 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 290 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 152 optimal weight: 20.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25519 Z= 0.245 Angle : 0.581 11.403 34674 Z= 0.285 Chirality : 0.045 0.379 4173 Planarity : 0.005 0.152 4302 Dihedral : 8.752 77.624 5213 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.31 % Allowed : 9.51 % Favored : 89.18 % 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: 0.15 (0.16), residues: 2991 helix: 1.09 (0.27), residues: 444 sheet: 0.04 (0.16), residues: 1032 loop : -0.03 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP W 427 HIS 0.006 0.001 HIS B 105 PHE 0.010 0.001 PHE O 103 TYR 0.016 0.001 TYR N 33 ARG 0.003 0.000 ARG F 147 *********************** 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 100 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 65 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 4 MET cc_start: 0.7256 (mmm) cc_final: 0.7053 (tpp) REVERT: M 42 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: S 519 PHE cc_start: 0.5795 (t80) cc_final: 0.5445 (t80) REVERT: S 584 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7494 (mt-10) REVERT: W 44 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9005 (m) REVERT: J 150 MET cc_start: 0.4516 (tpt) cc_final: 0.3935 (tpt) REVERT: O 131 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8139 (pptt) REVERT: O 174 LYS cc_start: 0.8335 (pttm) cc_final: 0.7411 (mppt) REVERT: Q 519 PHE cc_start: 0.6176 (t80) cc_final: 0.5939 (t80) REVERT: Q 530 MET cc_start: 0.7947 (mtp) cc_final: 0.7720 (mtt) REVERT: Q 584 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7706 (mt-10) outliers start: 35 outliers final: 20 residues processed: 94 average time/residue: 0.4180 time to fit residues: 63.2823 Evaluate side-chains 85 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 M residue 170 GLU Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain E residue 216 ASN 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 426 MET Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain Q residue 616 ASN 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 279 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 180 optimal weight: 30.0000 chunk 176 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 80 ASN ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 25519 Z= 0.313 Angle : 0.609 11.804 34674 Z= 0.301 Chirality : 0.046 0.391 4173 Planarity : 0.005 0.151 4302 Dihedral : 8.770 76.336 5213 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 1.12 % Allowed : 10.07 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (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: 0.02 (0.16), residues: 2991 helix: 0.96 (0.26), residues: 444 sheet: -0.11 (0.15), residues: 1068 loop : -0.03 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP W 427 HIS 0.005 0.001 HIS R 111 PHE 0.018 0.002 PHE J 93 TYR 0.017 0.001 TYR N 33 ARG 0.003 0.000 ARG R 100 *********************** 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 94 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: S 519 PHE cc_start: 0.5787 (t80) cc_final: 0.5430 (t80) REVERT: S 584 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7553 (mt-10) REVERT: W 44 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9008 (m) REVERT: J 150 MET cc_start: 0.4648 (tpt) cc_final: 0.4097 (tpt) REVERT: O 131 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8031 (pptt) REVERT: O 174 LYS cc_start: 0.8350 (pttm) cc_final: 0.7468 (mppt) REVERT: Q 519 PHE cc_start: 0.6211 (t80) cc_final: 0.5964 (t80) REVERT: Q 584 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7740 (mt-10) outliers start: 30 outliers final: 21 residues processed: 88 average time/residue: 0.3772 time to fit residues: 55.1616 Evaluate side-chains 87 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 170 GLU Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain S residue 616 ASN Chi-restraints excluded: chain W residue 44 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 426 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain E residue 216 ASN 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 467 THR Chi-restraints excluded: chain Q residue 616 ASN 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 178 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25519 Z= 0.280 Angle : 0.593 11.983 34674 Z= 0.291 Chirality : 0.046 0.386 4173 Planarity : 0.005 0.152 4302 Dihedral : 8.503 77.523 5213 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.39 % Allowed : 9.96 % 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: 0.00 (0.16), residues: 2991 helix: 0.97 (0.26), residues: 444 sheet: -0.15 (0.15), residues: 1068 loop : -0.04 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 427 HIS 0.004 0.001 HIS E 111 PHE 0.011 0.002 PHE W 468 TYR 0.015 0.001 TYR N 33 ARG 0.003 0.000 ARG J 476 *********************** 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 100 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 63 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: S 519 PHE cc_start: 0.5750 (t80) cc_final: 0.5407 (t80) REVERT: S 584 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7554 (mt-10) REVERT: W 44 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.9024 (m) REVERT: W 97 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8756 (mtmm) REVERT: B 104 MET cc_start: 0.9092 (ttt) cc_final: 0.8871 (ttt) REVERT: B 327 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: J 150 MET cc_start: 0.5172 (tpt) cc_final: 0.4638 (tpt) REVERT: O 174 LYS cc_start: 0.8260 (pttm) cc_final: 0.7361 (mppt) REVERT: Q 519 PHE cc_start: 0.6111 (t80) cc_final: 0.5872 (t80) REVERT: Q 584 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7743 (mt-10) outliers start: 37 outliers final: 24 residues processed: 93 average time/residue: 0.3789 time to fit residues: 58.0936 Evaluate side-chains 91 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 GLN Chi-restraints excluded: chain M residue 168 VAL 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 W residue 44 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 426 MET 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 325 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain E residue 216 ASN 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 Q residue 616 ASN 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 277 optimal weight: 30.0000 chunk 252 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 276 optimal weight: 0.0670 chunk 162 optimal weight: 10.0000 chunk 117 optimal weight: 0.0370 chunk 211 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS W 428 GLN ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 25519 Z= 0.166 Angle : 0.543 11.479 34674 Z= 0.266 Chirality : 0.044 0.365 4173 Planarity : 0.004 0.148 4302 Dihedral : 7.872 80.055 5213 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.12 % Allowed : 10.45 % Favored : 88.43 % 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 (0.16), residues: 2991 helix: 1.24 (0.27), residues: 444 sheet: -0.10 (0.15), residues: 1080 loop : 0.00 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J 427 HIS 0.002 0.001 HIS B 330 PHE 0.008 0.001 PHE F 144 TYR 0.012 0.001 TYR M 145 ARG 0.002 0.000 ARG J 429 *********************** 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 94 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: S 519 PHE cc_start: 0.5705 (t80) cc_final: 0.5394 (t80) REVERT: S 584 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7486 (mt-10) REVERT: W 44 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9029 (m) REVERT: W 97 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8749 (mtmm) REVERT: W 161 MET cc_start: 0.7998 (tpt) cc_final: 0.7606 (tpt) REVERT: B 104 MET cc_start: 0.8959 (ttt) cc_final: 0.8721 (ttt) REVERT: B 327 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (mtm180) REVERT: J 150 MET cc_start: 0.5113 (tpt) cc_final: 0.4609 (tpt) REVERT: O 131 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8038 (pptt) REVERT: O 174 LYS cc_start: 0.8223 (pttm) cc_final: 0.7294 (mppt) REVERT: Q 584 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7686 (mt-10) outliers start: 30 outliers final: 21 residues processed: 90 average time/residue: 0.3860 time to fit residues: 56.9633 Evaluate side-chains 89 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 W residue 44 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 426 MET 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 B residue 426 MET Chi-restraints excluded: chain B residue 427 TRP 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 Q residue 616 ASN 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 176 optimal weight: 10.0000 chunk 284 optimal weight: 40.0000 chunk 173 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 25519 Z= 0.388 Angle : 0.641 12.405 34674 Z= 0.312 Chirality : 0.047 0.378 4173 Planarity : 0.005 0.150 4302 Dihedral : 8.283 80.145 5213 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 1.01 % Allowed : 10.45 % 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: -0.08 (0.16), residues: 2991 helix: 0.95 (0.26), residues: 447 sheet: -0.20 (0.15), residues: 1071 loop : -0.11 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP W 427 HIS 0.005 0.001 HIS R 111 PHE 0.017 0.002 PHE O 103 TYR 0.018 0.002 TYR N 33 ARG 0.004 0.001 ARG M 113 ********************** 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 90 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: S 519 PHE cc_start: 0.5733 (t80) cc_final: 0.5399 (t80) REVERT: S 584 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7532 (mt-10) REVERT: S 626 MET cc_start: 0.7978 (ttm) cc_final: 0.7646 (ttp) REVERT: W 44 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9022 (m) REVERT: W 97 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (mtmm) REVERT: W 271 MET cc_start: 0.8428 (mmp) cc_final: 0.8216 (mmp) REVERT: B 104 MET cc_start: 0.9083 (ttt) cc_final: 0.8804 (ttt) REVERT: B 327 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7228 (mtp180) REVERT: J 150 MET cc_start: 0.5181 (tpt) cc_final: 0.4665 (tpt) REVERT: O 174 LYS cc_start: 0.8284 (pttm) cc_final: 0.7371 (mppt) REVERT: Q 584 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7748 (mt-10) outliers start: 27 outliers final: 21 residues processed: 85 average time/residue: 0.3714 time to fit residues: 52.8121 Evaluate side-chains 88 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 W residue 44 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 97 LYS Chi-restraints excluded: chain W residue 199 SER Chi-restraints excluded: chain W residue 286 VAL Chi-restraints excluded: chain W residue 325 ASP 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 325 ASP Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 427 TRP 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 Q residue 616 ASN 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 189 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 99 optimal weight: 0.0970 chunk 244 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 194 HIS S 652 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.048162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034224 restraints weight = 168411.689| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.85 r_work: 0.2897 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25519 Z= 0.246 Angle : 0.572 12.190 34674 Z= 0.280 Chirality : 0.045 0.363 4173 Planarity : 0.004 0.149 4302 Dihedral : 7.877 83.283 5213 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 0.97 % Allowed : 10.67 % Favored : 88.35 % 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: -0.06 (0.16), residues: 2991 helix: 1.07 (0.26), residues: 450 sheet: -0.22 (0.15), residues: 1080 loop : -0.11 (0.18), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP W 427 HIS 0.003 0.001 HIS B 330 PHE 0.010 0.001 PHE W 468 TYR 0.013 0.001 TYR N 33 ARG 0.003 0.000 ARG M 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.79 seconds wall clock time: 76 minutes 14.89 seconds (4574.89 seconds total)