Starting phenix.real_space_refine on Sat Dec 9 21:13:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zj8_14744/12_2023/7zj8_14744_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 57 5.16 5 C 7665 2.51 5 N 2088 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12342 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "B" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "D" 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: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "J" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "N" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.67, per 1000 atoms: 0.54 Number of scatterers: 12342 At special positions: 0 Unit cell: (97.2, 93.96, 149.04, 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 57 16.00 O 2532 8.00 N 2088 7.00 C 7665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.07 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.05 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.11 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.05 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.05 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.07 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.05 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.10 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.07 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.05 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.10 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.05 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG M 1 " - " FUC M 4 " NAG-ASN " NAG A 601 " - " ASN A 483 " " NAG A 602 " - " ASN A 22 " " NAG B 602 " - " ASN B 483 " " NAG B 603 " - " ASN B 22 " " NAG C 602 " - " ASN C 483 " " NAG C 603 " - " ASN C 22 " " NAG D 1 " - " ASN A 38 " " NAG E 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 285 " " NAG H 1 " - " ASN B 38 " " NAG I 1 " - " ASN B 81 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN B 285 " " NAG L 1 " - " ASN C 38 " " NAG M 1 " - " ASN C 81 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.3 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 30 sheets defined 24.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.736A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.824A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 405 through 454 removed outlier: 3.517A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 448 " --> pdb=" O MET A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 488 through 499 removed outlier: 5.306A pdb=" N ASP A 493 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 494 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.737A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 74 through 79' Processing helix chain 'B' and resid 105 through 115 Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.822A pdb=" N THR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 405 through 454 removed outlier: 3.514A pdb=" N VAL B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 488 through 499 removed outlier: 5.305A pdb=" N ASP B 493 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 494 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.736A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 79' Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.825A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 405 through 454 removed outlier: 3.515A pdb=" N VAL C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 448 " --> pdb=" O MET C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 488 through 499 removed outlier: 5.306A pdb=" N ASP C 493 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 494 " --> pdb=" O TYR C 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 361 through 365 Processing sheet with id= B, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= D, first strand: chain 'A' and resid 50 through 52 No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 58 through 60 removed outlier: 7.034A pdb=" N LEU A 86 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER A 266 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU A 89 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET A 268 " --> pdb=" O GLU A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 120 through 122 Processing sheet with id= G, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= H, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.959A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 176 through 184 Processing sheet with id= J, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.454A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 361 through 365 Processing sheet with id= L, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= N, first strand: chain 'B' and resid 50 through 52 No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 58 through 60 removed outlier: 7.034A pdb=" N LEU B 86 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER B 266 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU B 89 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET B 268 " --> pdb=" O GLU B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 120 through 122 Processing sheet with id= Q, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= R, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.957A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 176 through 184 Processing sheet with id= T, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.455A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 361 through 365 Processing sheet with id= V, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= X, first strand: chain 'C' and resid 50 through 52 No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'C' and resid 58 through 60 removed outlier: 7.037A pdb=" N LEU C 86 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER C 266 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU C 89 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET C 268 " --> pdb=" O GLU C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= AA, first strand: chain 'C' and resid 151 through 153 Processing sheet with id= AB, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.957A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 176 through 184 Processing sheet with id= AD, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.456A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1089 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: 3.82 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2040 1.31 - 1.44: 3525 1.44 - 1.57: 6942 1.57 - 1.71: 0 1.71 - 1.84: 78 Bond restraints: 12585 Sorted by residual: bond pdb=" C GLN B 295 " pdb=" O GLN B 295 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.22e-02 6.72e+03 1.95e+01 bond pdb=" C GLN A 295 " pdb=" O GLN A 295 " ideal model delta sigma weight residual 1.234 1.181 0.052 1.22e-02 6.72e+03 1.85e+01 bond pdb=" C GLN C 295 " pdb=" O GLN C 295 " ideal model delta sigma weight residual 1.234 1.182 0.052 1.22e-02 6.72e+03 1.80e+01 bond pdb=" C LEU A 42 " pdb=" O LEU A 42 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.33e-02 5.65e+03 1.77e+01 bond pdb=" C LEU B 42 " pdb=" O LEU B 42 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.33e-02 5.65e+03 1.74e+01 ... (remaining 12580 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.77: 298 105.77 - 113.02: 6486 113.02 - 120.27: 5746 120.27 - 127.52: 4421 127.52 - 134.77: 110 Bond angle restraints: 17061 Sorted by residual: angle pdb=" CA GLN C 295 " pdb=" C GLN C 295 " pdb=" O GLN C 295 " ideal model delta sigma weight residual 121.33 114.58 6.75 1.08e+00 8.57e-01 3.90e+01 angle pdb=" CA GLN A 295 " pdb=" C GLN A 295 " pdb=" O GLN A 295 " ideal model delta sigma weight residual 121.33 114.60 6.73 1.08e+00 8.57e-01 3.88e+01 angle pdb=" CA GLN B 295 " pdb=" C GLN B 295 " pdb=" O GLN B 295 " ideal model delta sigma weight residual 121.33 114.67 6.66 1.08e+00 8.57e-01 3.81e+01 angle pdb=" CA PHE C 294 " pdb=" C PHE C 294 " pdb=" O PHE C 294 " ideal model delta sigma weight residual 121.73 114.28 7.45 1.35e+00 5.49e-01 3.04e+01 angle pdb=" CA ASN A 382 " pdb=" C ASN A 382 " pdb=" O ASN A 382 " ideal model delta sigma weight residual 120.70 115.07 5.63 1.03e+00 9.43e-01 2.99e+01 ... (remaining 17056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 6829 15.62 - 31.24: 833 31.24 - 46.86: 147 46.86 - 62.48: 66 62.48 - 78.10: 15 Dihedral angle restraints: 7890 sinusoidal: 3633 harmonic: 4257 Sorted by residual: dihedral pdb=" CA ASP B 60 " pdb=" C ASP B 60 " pdb=" N GLY B 61 " pdb=" CA GLY B 61 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU B 455 " pdb=" C LEU B 455 " pdb=" N ARG B 456 " pdb=" CA ARG B 456 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP C 60 " pdb=" C ASP C 60 " pdb=" N GLY C 61 " pdb=" CA GLY C 61 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 7887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1708 0.138 - 0.276: 304 0.276 - 0.414: 7 0.414 - 0.551: 3 0.551 - 0.689: 3 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.85e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.83e+01 chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.58e+01 ... (remaining 2022 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.333 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A 601 " -0.155 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.486 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.331 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 602 " -0.153 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.485 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.328 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C7 NAG C 602 " -0.154 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.482 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.253 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 3 2.16 - 2.84: 2719 2.84 - 3.53: 15671 3.53 - 4.21: 28577 4.21 - 4.90: 46241 Nonbonded interactions: 93211 Sorted by model distance: nonbonded pdb=" O ASN B 8 " pdb=" NZ LYS B 472 " model vdw 1.471 2.520 nonbonded pdb=" O ASN A 8 " pdb=" NZ LYS A 472 " model vdw 1.473 2.520 nonbonded pdb=" O ASN C 8 " pdb=" NZ LYS C 472 " model vdw 1.474 2.520 nonbonded pdb=" N GLN C 295 " pdb=" O GLN C 295 " model vdw 2.412 2.496 nonbonded pdb=" N GLN B 295 " pdb=" O GLN B 295 " model vdw 2.412 2.496 ... (remaining 93206 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' and (resid 8 through 501 or resid 602)) selection = (chain 'B' and (resid 8 through 501 or resid 602)) selection = (chain 'C' and (resid 8 through 501 or resid 602)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.480 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.350 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 0.056 12585 Z= 0.907 Angle : 1.871 11.117 17061 Z= 1.311 Chirality : 0.101 0.689 2025 Planarity : 0.017 0.296 2154 Dihedral : 14.462 78.095 5106 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.23 % Allowed : 10.44 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.59 (0.18), residues: 1476 helix: -1.26 (0.24), residues: 357 sheet: -0.93 (0.29), residues: 288 loop : -2.28 (0.16), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.007 TRP C 421 HIS 0.013 0.005 HIS A 435 PHE 0.040 0.006 PHE A 258 TYR 0.040 0.006 TYR A 161 ARG 0.012 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.359 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.3279 time to fit residues: 69.5534 Evaluate side-chains 48 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 6.9990 chunk 111 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 33 GLN A 54 ASN A 248 ASN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS B 8 ASN B 54 ASN B 248 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS C 8 ASN C 33 GLN C 54 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS C 497 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12585 Z= 0.166 Angle : 0.602 8.860 17061 Z= 0.311 Chirality : 0.043 0.225 2025 Planarity : 0.004 0.055 2154 Dihedral : 6.755 56.642 2325 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.31 % Allowed : 11.52 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.80 (0.19), residues: 1476 helix: 1.42 (0.27), residues: 354 sheet: -0.04 (0.28), residues: 306 loop : -1.69 (0.17), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 180 HIS 0.007 0.002 HIS A 471 PHE 0.010 0.001 PHE B 392 TYR 0.012 0.001 TYR A 105 ARG 0.005 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 1.522 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 76 average time/residue: 0.2887 time to fit residues: 31.7270 Evaluate side-chains 55 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1413 time to fit residues: 3.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12585 Z= 0.371 Angle : 0.673 9.873 17061 Z= 0.343 Chirality : 0.047 0.304 2025 Planarity : 0.005 0.039 2154 Dihedral : 6.841 58.506 2325 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.93 % Allowed : 12.30 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.20), residues: 1476 helix: 1.79 (0.27), residues: 354 sheet: 0.18 (0.28), residues: 327 loop : -1.55 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 421 HIS 0.007 0.002 HIS A 184 PHE 0.018 0.002 PHE C 258 TYR 0.011 0.002 TYR A 178 ARG 0.004 0.001 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 1.382 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 75 average time/residue: 0.2934 time to fit residues: 31.5825 Evaluate side-chains 62 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 1.355 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1174 time to fit residues: 5.5644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12585 Z= 0.200 Angle : 0.551 9.695 17061 Z= 0.277 Chirality : 0.042 0.265 2025 Planarity : 0.004 0.032 2154 Dihedral : 6.466 57.489 2325 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.93 % Allowed : 13.15 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.07 (0.21), residues: 1476 helix: 2.25 (0.28), residues: 354 sheet: 0.27 (0.28), residues: 324 loop : -1.31 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.006 0.001 HIS A 75 PHE 0.011 0.002 PHE A 258 TYR 0.009 0.001 TYR A 105 ARG 0.004 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 1.426 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.3114 time to fit residues: 25.9013 Evaluate side-chains 50 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1931 time to fit residues: 3.3441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 HIS C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12585 Z= 0.317 Angle : 0.610 9.927 17061 Z= 0.307 Chirality : 0.045 0.277 2025 Planarity : 0.004 0.035 2154 Dihedral : 6.505 59.344 2325 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.85 % Allowed : 14.15 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.16 (0.21), residues: 1476 helix: 2.17 (0.28), residues: 354 sheet: 0.12 (0.28), residues: 339 loop : -1.34 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.006 0.002 HIS B 17 PHE 0.015 0.002 PHE C 392 TYR 0.009 0.002 TYR A 105 ARG 0.003 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 1.420 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 58 average time/residue: 0.3078 time to fit residues: 25.8577 Evaluate side-chains 50 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1242 time to fit residues: 3.2687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12585 Z= 0.134 Angle : 0.495 9.582 17061 Z= 0.246 Chirality : 0.040 0.256 2025 Planarity : 0.003 0.032 2154 Dihedral : 6.095 56.367 2325 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.46 % Allowed : 14.46 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.20 (0.21), residues: 1476 helix: 2.77 (0.28), residues: 354 sheet: 0.28 (0.28), residues: 345 loop : -1.26 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 421 HIS 0.005 0.001 HIS A 75 PHE 0.007 0.001 PHE A 500 TYR 0.008 0.001 TYR B 105 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.482 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 0.2920 time to fit residues: 23.4203 Evaluate side-chains 45 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1121 time to fit residues: 2.0849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12585 Z= 0.289 Angle : 0.562 9.804 17061 Z= 0.281 Chirality : 0.044 0.271 2025 Planarity : 0.004 0.035 2154 Dihedral : 6.438 59.600 2325 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.54 % Allowed : 14.39 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.10 (0.21), residues: 1476 helix: 2.60 (0.28), residues: 351 sheet: 0.18 (0.28), residues: 339 loop : -1.23 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.008 0.001 HIS C 17 PHE 0.013 0.002 PHE B 87 TYR 0.008 0.001 TYR C 105 ARG 0.004 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.381 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.2983 time to fit residues: 23.5160 Evaluate side-chains 48 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1999 time to fit residues: 2.9935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12585 Z= 0.262 Angle : 0.551 9.758 17061 Z= 0.276 Chirality : 0.043 0.266 2025 Planarity : 0.004 0.037 2154 Dihedral : 6.607 59.494 2325 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.08 % Allowed : 15.00 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.07 (0.21), residues: 1476 helix: 2.56 (0.27), residues: 351 sheet: 0.13 (0.28), residues: 339 loop : -1.23 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.005 0.001 HIS B 17 PHE 0.011 0.002 PHE B 392 TYR 0.009 0.001 TYR C 105 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.281 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.3500 time to fit residues: 22.4695 Evaluate side-chains 43 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.0270 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12585 Z= 0.156 Angle : 0.499 9.618 17061 Z= 0.248 Chirality : 0.041 0.259 2025 Planarity : 0.003 0.034 2154 Dihedral : 6.360 57.261 2325 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.28 (0.22), residues: 1476 helix: 2.90 (0.27), residues: 351 sheet: 0.32 (0.28), residues: 345 loop : -1.23 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.005 0.001 HIS C 17 PHE 0.009 0.001 PHE B 392 TYR 0.008 0.001 TYR C 105 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.561 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.3343 time to fit residues: 22.7396 Evaluate side-chains 45 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12585 Z= 0.290 Angle : 0.565 9.806 17061 Z= 0.282 Chirality : 0.044 0.272 2025 Planarity : 0.004 0.038 2154 Dihedral : 6.676 59.964 2325 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.08 % Allowed : 15.00 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.21), residues: 1476 helix: 2.62 (0.28), residues: 345 sheet: 0.20 (0.29), residues: 324 loop : -1.20 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.009 0.001 HIS C 17 PHE 0.013 0.002 PHE B 87 TYR 0.009 0.001 TYR C 105 ARG 0.002 0.000 ARG B 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.536 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.3330 time to fit residues: 23.1988 Evaluate side-chains 44 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1692 time to fit residues: 2.2683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.075649 restraints weight = 22297.556| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.89 r_work: 0.2843 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12585 Z= 0.157 Angle : 0.496 9.592 17061 Z= 0.246 Chirality : 0.041 0.259 2025 Planarity : 0.003 0.035 2154 Dihedral : 6.389 59.690 2325 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.28 (0.22), residues: 1476 helix: 2.91 (0.27), residues: 351 sheet: 0.31 (0.28), residues: 345 loop : -1.22 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.007 0.001 HIS C 17 PHE 0.008 0.001 PHE B 392 TYR 0.008 0.001 TYR A 105 ARG 0.002 0.000 ARG B 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2367.69 seconds wall clock time: 44 minutes 16.07 seconds (2656.07 seconds total)