Starting phenix.real_space_refine on Sat Mar 16 22:13:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/03_2024/7l8w_23238_updated.pdb" } resolution = 4.1 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 105 5.16 5 C 9845 2.51 5 N 2677 2.21 5 O 3176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3485 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1060 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3466 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "J" 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: 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: "M" 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: "N" 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: "O" 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: "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: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" 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: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "D" 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: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "F" 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: 8.88, per 1000 atoms: 0.56 Number of scatterers: 15803 At special positions: 0 Unit cell: (127.72, 136.99, 118.45, 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 105 16.00 O 3176 8.00 N 2677 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.10 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 8 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 9 " " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 160 " " NAG A 613 " - " ASN A 197 " " NAG A 614 " - " ASN A 133 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 137 " " NAG A 617 " - " ASN A 363 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG C 616 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN E 332 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 156 " Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 2.5 seconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 32 sheets defined 28.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.732A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.158A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.890A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'B' and resid 532 through 544 removed outlier: 5.138A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 622 No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 628 through 660 removed outlier: 3.514A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.743A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.631A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 483 " --> pdb=" O ARG C 480 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.345A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 530 through 545 removed outlier: 4.385A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 662 removed outlier: 5.443A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 661 " --> pdb=" O GLN D 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 662 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.762A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 485 removed outlier: 3.659A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.117A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 532 through 545 removed outlier: 3.954A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 567 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 662 removed outlier: 6.277A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.665A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.315A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.351A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.445A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= N, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= P, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= Q, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.795A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.694A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 304 through 307 Processing sheet with id= T, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= V, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= X, first strand: chain 'E' and resid 169 through 177 removed outlier: 4.720A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.320A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 304 through 307 Processing sheet with id= AC, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.778A pdb=" N UNK H 18 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 106 through 109 Processing sheet with id= AE, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= AF, first strand: chain 'L' and resid 36 through 40 removed outlier: 3.605A pdb=" N UNK L 86 " --> pdb=" O UNK L 40 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3102 1.32 - 1.46: 5297 1.46 - 1.60: 7510 1.60 - 1.74: 30 1.74 - 1.88: 133 Bond restraints: 16072 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG C 550 " pdb=" CZ ARG C 550 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 95.23 - 103.10: 152 103.10 - 110.98: 6444 110.98 - 118.86: 7248 118.86 - 126.74: 7760 126.74 - 134.62: 248 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C PHE C 53 " pdb=" N CYS C 54 " pdb=" CA CYS C 54 " ideal model delta sigma weight residual 122.19 133.63 -11.44 1.41e+00 5.03e-01 6.59e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.01e+00 9.80e-01 6.44e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.05 7.42 9.60e-01 1.09e+00 5.98e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.23 122.33 -9.10 1.24e+00 6.50e-01 5.39e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10478 21.43 - 42.86: 220 42.86 - 64.30: 74 64.30 - 85.73: 33 85.73 - 107.16: 13 Dihedral angle restraints: 10818 sinusoidal: 5229 harmonic: 5589 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.12 -73.12 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 164.19 -71.19 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 10815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2395 0.188 - 0.376: 311 0.376 - 0.565: 64 0.565 - 0.753: 1 0.753 - 0.941: 2 Chirality restraints: 2773 Sorted by residual: chirality pdb=" C1 MAN G 8 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 8 " pdb=" O5 MAN G 8 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.21e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 2770 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 602 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.332 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A 607 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 612 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A 612 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 612 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 612 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG A 612 " 0.060 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5764 2.88 - 3.39: 14426 3.39 - 3.89: 25578 3.89 - 4.40: 29240 4.40 - 4.90: 45970 Nonbonded interactions: 120978 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.378 2.496 nonbonded pdb=" O3 NAG D 703 " pdb=" O7 NAG D 703 " model vdw 2.383 2.440 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.436 2.520 nonbonded pdb=" OD1 ASN E 234 " pdb=" N GLY E 235 " model vdw 2.451 2.520 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.488 2.520 ... (remaining 120973 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 33 through 57 or resid 64 through 503 or resid 601 through \ 616)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 457 or resid 461 throu \ gh 550 or resid 601 through 616)) selection = (chain 'E' and (resid 33 through 57 or resid 64 through 457 or resid 461 through \ 503 or resid 601 through 616)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 558 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 662 or resid 702 through 703)) } ncs_group { reference = (chain 'H' and resid 8 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 10.600 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.370 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.140 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.021 0.121 16072 Z= 1.338 Angle : 1.709 11.444 21852 Z= 1.104 Chirality : 0.137 0.941 2773 Planarity : 0.018 0.291 2679 Dihedral : 11.366 107.162 7070 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.19), residues: 1678 helix: 0.58 (0.22), residues: 427 sheet: 1.21 (0.23), residues: 465 loop : 0.77 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.010 TRP C 35 HIS 0.013 0.002 HIS A 249 PHE 0.039 0.006 PHE A 383 TYR 0.071 0.008 TYR D 638 ARG 0.006 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 1.691 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: A 199 SER cc_start: 0.9435 (p) cc_final: 0.8917 (t) REVERT: A 257 THR cc_start: 0.8957 (p) cc_final: 0.8655 (m) REVERT: B 591 GLN cc_start: 0.9098 (tt0) cc_final: 0.8843 (tt0) REVERT: B 599 SER cc_start: 0.9019 (p) cc_final: 0.8341 (t) REVERT: B 601 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8597 (tptp) REVERT: B 603 ILE cc_start: 0.8779 (mt) cc_final: 0.8504 (mp) REVERT: C 38 VAL cc_start: 0.8541 (t) cc_final: 0.8184 (t) REVERT: C 69 TRP cc_start: 0.8141 (m-10) cc_final: 0.7916 (m-10) REVERT: C 102 GLU cc_start: 0.8251 (tp30) cc_final: 0.7744 (tm-30) REVERT: C 199 SER cc_start: 0.9546 (p) cc_final: 0.9297 (t) REVERT: D 585 ARG cc_start: 0.9197 (mmt180) cc_final: 0.8895 (ttm-80) REVERT: D 586 TYR cc_start: 0.9636 (t80) cc_final: 0.9361 (t80) REVERT: D 623 TRP cc_start: 0.8861 (m100) cc_final: 0.8397 (m-10) REVERT: E 45 TRP cc_start: 0.8802 (p90) cc_final: 0.8588 (p90) REVERT: E 57 ASP cc_start: 0.8224 (t0) cc_final: 0.7880 (p0) REVERT: E 103 GLN cc_start: 0.8566 (tt0) cc_final: 0.8209 (tm-30) REVERT: E 381 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7550 (tt0) REVERT: F 579 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8779 (ttm170) REVERT: F 629 LEU cc_start: 0.9059 (tp) cc_final: 0.8768 (mp) REVERT: F 638 TYR cc_start: 0.8321 (m-80) cc_final: 0.8061 (m-10) REVERT: F 650 GLN cc_start: 0.8917 (tp40) cc_final: 0.7738 (tm-30) REVERT: F 654 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7130 (mt-10) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3072 time to fit residues: 221.8327 Evaluate side-chains 249 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 302 ASN C 422 GLN D 591 GLN E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16072 Z= 0.237 Angle : 0.752 10.340 21852 Z= 0.381 Chirality : 0.052 0.695 2773 Planarity : 0.004 0.043 2679 Dihedral : 9.697 91.465 3805 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.31 % Favored : 98.63 % Rotamer: Outliers : 0.26 % Allowed : 1.90 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.20), residues: 1678 helix: 1.46 (0.25), residues: 422 sheet: 1.24 (0.23), residues: 443 loop : 0.23 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 479 HIS 0.008 0.002 HIS F 564 PHE 0.018 0.002 PHE A 383 TYR 0.018 0.002 TYR A 191 ARG 0.006 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 372 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.8343 (m-30) cc_final: 0.8101 (t0) REVERT: A 209 SER cc_start: 0.8701 (t) cc_final: 0.8340 (p) REVERT: A 475 MET cc_start: 0.9017 (mmm) cc_final: 0.8746 (mmm) REVERT: B 568 LEU cc_start: 0.8591 (mp) cc_final: 0.8285 (mp) REVERT: B 599 SER cc_start: 0.9005 (p) cc_final: 0.8164 (t) REVERT: B 601 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8508 (tptp) REVERT: B 602 LEU cc_start: 0.8857 (mt) cc_final: 0.8498 (pt) REVERT: B 626 MET cc_start: 0.4571 (mmm) cc_final: 0.4255 (mmt) REVERT: B 634 GLU cc_start: 0.8180 (pt0) cc_final: 0.7860 (pt0) REVERT: B 641 ILE cc_start: 0.8105 (mp) cc_final: 0.7619 (tp) REVERT: B 643 TYR cc_start: 0.9066 (m-10) cc_final: 0.8775 (m-10) REVERT: C 38 VAL cc_start: 0.8549 (t) cc_final: 0.7979 (t) REVERT: C 114 GLN cc_start: 0.8639 (tp40) cc_final: 0.7794 (tm-30) REVERT: C 199 SER cc_start: 0.9520 (p) cc_final: 0.9196 (t) REVERT: C 286 VAL cc_start: 0.9368 (t) cc_final: 0.9145 (m) REVERT: C 377 ASN cc_start: 0.9287 (t0) cc_final: 0.8972 (t0) REVERT: C 395 TRP cc_start: 0.7927 (m100) cc_final: 0.7658 (m100) REVERT: C 486 TYR cc_start: 0.9092 (m-80) cc_final: 0.8774 (m-80) REVERT: D 565 LEU cc_start: 0.8095 (tp) cc_final: 0.7697 (tp) REVERT: D 577 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8016 (tm-30) REVERT: D 588 ARG cc_start: 0.8933 (tmm-80) cc_final: 0.8685 (tmm-80) REVERT: E 51 THR cc_start: 0.9188 (m) cc_final: 0.8764 (p) REVERT: E 57 ASP cc_start: 0.8087 (t0) cc_final: 0.7828 (p0) REVERT: E 103 GLN cc_start: 0.8477 (tt0) cc_final: 0.7954 (tm-30) REVERT: E 168 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8832 (ttpt) REVERT: F 543 ASN cc_start: 0.8150 (t0) cc_final: 0.7830 (t0) REVERT: F 590 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9050 (tp40) REVERT: F 629 LEU cc_start: 0.8890 (tp) cc_final: 0.8556 (mp) REVERT: F 634 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8079 (mm-30) REVERT: F 650 GLN cc_start: 0.9035 (tp40) cc_final: 0.8402 (tm-30) REVERT: F 652 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8339 (tt0) REVERT: F 653 GLN cc_start: 0.8489 (tt0) cc_final: 0.8239 (tt0) outliers start: 4 outliers final: 2 residues processed: 374 average time/residue: 0.2674 time to fit residues: 147.5517 Evaluate side-chains 256 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 16072 Z= 0.441 Angle : 0.832 12.717 21852 Z= 0.414 Chirality : 0.052 0.428 2773 Planarity : 0.005 0.059 2679 Dihedral : 9.176 75.960 3805 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 0.33 % Allowed : 3.60 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.20), residues: 1678 helix: 0.92 (0.25), residues: 424 sheet: 0.83 (0.24), residues: 451 loop : -0.11 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 571 HIS 0.007 0.002 HIS A 330 PHE 0.023 0.003 PHE A 361 TYR 0.020 0.002 TYR C 191 ARG 0.008 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 300 time to evaluate : 1.747 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: A 101 VAL cc_start: 0.9462 (m) cc_final: 0.9192 (p) REVERT: A 104 MET cc_start: 0.9261 (tpp) cc_final: 0.8829 (tpp) REVERT: A 194 ILE cc_start: 0.9358 (tt) cc_final: 0.9157 (mm) REVERT: A 209 SER cc_start: 0.8859 (t) cc_final: 0.8633 (p) REVERT: A 256 SER cc_start: 0.9501 (p) cc_final: 0.9142 (m) REVERT: B 599 SER cc_start: 0.9099 (p) cc_final: 0.8398 (t) REVERT: B 602 LEU cc_start: 0.8522 (mt) cc_final: 0.8274 (pt) REVERT: B 628 TRP cc_start: 0.8102 (m100) cc_final: 0.7874 (m100) REVERT: B 641 ILE cc_start: 0.8121 (mp) cc_final: 0.7787 (tp) REVERT: B 643 TYR cc_start: 0.9086 (m-10) cc_final: 0.8768 (m-10) REVERT: C 38 VAL cc_start: 0.8741 (t) cc_final: 0.8460 (t) REVERT: C 98 ASN cc_start: 0.9217 (t0) cc_final: 0.8962 (t0) REVERT: C 151 ARG cc_start: 0.6877 (mtt-85) cc_final: 0.6615 (mtp85) REVERT: C 161 MET cc_start: 0.8806 (tpp) cc_final: 0.8602 (tpt) REVERT: C 199 SER cc_start: 0.9510 (p) cc_final: 0.9235 (t) REVERT: C 377 ASN cc_start: 0.9410 (t0) cc_final: 0.9209 (t0) REVERT: D 565 LEU cc_start: 0.8328 (tp) cc_final: 0.7893 (tp) REVERT: D 577 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 587 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9414 (mm) REVERT: D 588 ARG cc_start: 0.9106 (tmm-80) cc_final: 0.8841 (tmm-80) REVERT: D 615 SER cc_start: 0.8485 (t) cc_final: 0.8268 (m) REVERT: D 650 GLN cc_start: 0.8580 (tp40) cc_final: 0.8007 (tm-30) REVERT: F 530 MET cc_start: 0.8449 (mpp) cc_final: 0.8221 (mpp) REVERT: F 607 ASN cc_start: 0.8848 (p0) cc_final: 0.8474 (p0) REVERT: F 629 LEU cc_start: 0.8924 (tp) cc_final: 0.8590 (tp) REVERT: F 634 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8107 (mm-30) outliers start: 5 outliers final: 1 residues processed: 305 average time/residue: 0.2892 time to fit residues: 127.2397 Evaluate side-chains 222 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 9.9990 chunk 129 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16072 Z= 0.192 Angle : 0.630 12.544 21852 Z= 0.315 Chirality : 0.047 0.361 2773 Planarity : 0.004 0.042 2679 Dihedral : 8.127 65.606 3805 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.20 % Allowed : 1.51 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.20), residues: 1678 helix: 1.12 (0.26), residues: 426 sheet: 0.82 (0.24), residues: 444 loop : -0.13 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 69 HIS 0.004 0.001 HIS D 564 PHE 0.013 0.002 PHE E 376 TYR 0.014 0.001 TYR E 39 ARG 0.008 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 299 time to evaluate : 1.628 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: A 104 MET cc_start: 0.9031 (tpp) cc_final: 0.8561 (tpp) REVERT: A 256 SER cc_start: 0.9428 (p) cc_final: 0.9111 (m) REVERT: B 588 ARG cc_start: 0.8285 (ttt180) cc_final: 0.8080 (ttt180) REVERT: B 599 SER cc_start: 0.9086 (p) cc_final: 0.8316 (t) REVERT: B 601 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8513 (tptp) REVERT: B 602 LEU cc_start: 0.8774 (mt) cc_final: 0.8457 (pt) REVERT: B 641 ILE cc_start: 0.8131 (mp) cc_final: 0.7757 (tp) REVERT: B 643 TYR cc_start: 0.9106 (m-10) cc_final: 0.8830 (m-10) REVERT: C 38 VAL cc_start: 0.8565 (t) cc_final: 0.8244 (t) REVERT: C 199 SER cc_start: 0.9512 (p) cc_final: 0.9207 (t) REVERT: C 377 ASN cc_start: 0.9375 (t0) cc_final: 0.9019 (t0) REVERT: C 414 ILE cc_start: 0.9350 (mm) cc_final: 0.9060 (tp) REVERT: D 535 MET cc_start: 0.8128 (ptp) cc_final: 0.7891 (ptp) REVERT: D 571 TRP cc_start: 0.7359 (t60) cc_final: 0.6926 (t60) REVERT: D 577 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8154 (tm-30) REVERT: D 588 ARG cc_start: 0.9049 (tmm-80) cc_final: 0.8818 (tmm-80) REVERT: D 650 GLN cc_start: 0.8418 (tp40) cc_final: 0.7906 (tm-30) REVERT: E 150 MET cc_start: 0.8477 (mmm) cc_final: 0.8001 (mmt) REVERT: E 256 SER cc_start: 0.9421 (p) cc_final: 0.9161 (m) REVERT: E 308 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8353 (mtm180) REVERT: E 381 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7590 (tt0) REVERT: F 530 MET cc_start: 0.8503 (mpp) cc_final: 0.8233 (mpp) REVERT: F 607 ASN cc_start: 0.8814 (p0) cc_final: 0.8333 (p0) REVERT: F 629 LEU cc_start: 0.8934 (tp) cc_final: 0.8574 (mp) REVERT: F 634 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8049 (mm-30) REVERT: F 648 GLU cc_start: 0.8436 (tp30) cc_final: 0.8183 (tp30) outliers start: 3 outliers final: 1 residues processed: 301 average time/residue: 0.2761 time to fit residues: 121.3755 Evaluate side-chains 226 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 0.0070 chunk 75 optimal weight: 0.1980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16072 Z= 0.164 Angle : 0.579 13.287 21852 Z= 0.291 Chirality : 0.046 0.419 2773 Planarity : 0.004 0.045 2679 Dihedral : 7.257 58.456 3805 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.33 % Rotamer: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.20), residues: 1678 helix: 1.16 (0.26), residues: 424 sheet: 0.73 (0.24), residues: 433 loop : -0.13 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 69 HIS 0.004 0.001 HIS D 564 PHE 0.026 0.002 PHE A 468 TYR 0.016 0.001 TYR E 173 ARG 0.007 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8950 (tpp) cc_final: 0.8520 (tpp) REVERT: A 150 MET cc_start: 0.9007 (mtp) cc_final: 0.8807 (mtm) REVERT: A 256 SER cc_start: 0.9349 (p) cc_final: 0.9084 (m) REVERT: A 315 GLN cc_start: 0.8688 (mp10) cc_final: 0.8289 (mp10) REVERT: B 535 MET cc_start: 0.8124 (mpp) cc_final: 0.7419 (mmm) REVERT: B 584 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 588 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7423 (ttp-170) REVERT: B 599 SER cc_start: 0.9049 (p) cc_final: 0.8319 (t) REVERT: B 601 LYS cc_start: 0.8843 (ptpt) cc_final: 0.8466 (tptp) REVERT: B 602 LEU cc_start: 0.8648 (mt) cc_final: 0.8400 (pt) REVERT: B 634 GLU cc_start: 0.8465 (pt0) cc_final: 0.7540 (pp20) REVERT: B 641 ILE cc_start: 0.8122 (mp) cc_final: 0.7531 (tp) REVERT: B 643 TYR cc_start: 0.9093 (m-10) cc_final: 0.8875 (m-10) REVERT: C 38 VAL cc_start: 0.8374 (t) cc_final: 0.8084 (t) REVERT: C 199 SER cc_start: 0.9514 (p) cc_final: 0.9095 (t) REVERT: C 258 GLN cc_start: 0.8778 (mt0) cc_final: 0.8373 (tt0) REVERT: C 377 ASN cc_start: 0.9372 (t0) cc_final: 0.9004 (t0) REVERT: D 542 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7839 (tpt170) REVERT: D 577 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 588 ARG cc_start: 0.9028 (tmm-80) cc_final: 0.8814 (tmm-80) REVERT: D 615 SER cc_start: 0.8444 (t) cc_final: 0.8107 (m) REVERT: E 104 MET cc_start: 0.9121 (ttt) cc_final: 0.8857 (tpp) REVERT: E 150 MET cc_start: 0.8439 (mmm) cc_final: 0.8110 (mmt) REVERT: E 161 MET cc_start: 0.9083 (tpp) cc_final: 0.8408 (ttm) REVERT: E 256 SER cc_start: 0.9396 (p) cc_final: 0.9189 (m) REVERT: F 607 ASN cc_start: 0.8801 (p0) cc_final: 0.8254 (p0) REVERT: F 629 LEU cc_start: 0.9058 (tp) cc_final: 0.8702 (tp) REVERT: F 634 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8093 (mm-30) REVERT: F 648 GLU cc_start: 0.8419 (tp30) cc_final: 0.8158 (tp30) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.2671 time to fit residues: 115.9107 Evaluate side-chains 225 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.0770 chunk 164 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 352 HIS E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 462 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16072 Z= 0.197 Angle : 0.594 16.043 21852 Z= 0.298 Chirality : 0.046 0.405 2773 Planarity : 0.004 0.060 2679 Dihedral : 7.018 56.466 3805 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.21), residues: 1678 helix: 1.21 (0.27), residues: 424 sheet: 0.71 (0.25), residues: 433 loop : -0.18 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 69 HIS 0.006 0.001 HIS E 249 PHE 0.014 0.002 PHE A 468 TYR 0.017 0.001 TYR C 486 ARG 0.016 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9017 (tpp) cc_final: 0.8605 (tpp) REVERT: A 150 MET cc_start: 0.9025 (mtp) cc_final: 0.8822 (mtm) REVERT: A 256 SER cc_start: 0.9431 (p) cc_final: 0.9121 (m) REVERT: A 315 GLN cc_start: 0.8691 (mp10) cc_final: 0.8436 (mp10) REVERT: B 535 MET cc_start: 0.8100 (mpp) cc_final: 0.7452 (mmm) REVERT: B 588 ARG cc_start: 0.8311 (ttt180) cc_final: 0.7331 (ttm-80) REVERT: B 599 SER cc_start: 0.9037 (p) cc_final: 0.8364 (t) REVERT: B 602 LEU cc_start: 0.8649 (mt) cc_final: 0.8426 (pt) REVERT: B 634 GLU cc_start: 0.8607 (pt0) cc_final: 0.7898 (pp20) REVERT: B 641 ILE cc_start: 0.8155 (mp) cc_final: 0.7781 (tp) REVERT: C 38 VAL cc_start: 0.8423 (t) cc_final: 0.8141 (t) REVERT: C 199 SER cc_start: 0.9167 (p) cc_final: 0.8863 (m) REVERT: C 258 GLN cc_start: 0.8787 (mt0) cc_final: 0.8408 (tt0) REVERT: D 535 MET cc_start: 0.8094 (ptp) cc_final: 0.7863 (ptp) REVERT: D 542 ARG cc_start: 0.8681 (ttp80) cc_final: 0.7915 (tpt170) REVERT: D 565 LEU cc_start: 0.8121 (tp) cc_final: 0.7785 (tp) REVERT: D 571 TRP cc_start: 0.7326 (t60) cc_final: 0.6816 (t60) REVERT: D 615 SER cc_start: 0.8476 (t) cc_final: 0.8136 (m) REVERT: D 650 GLN cc_start: 0.8407 (tp40) cc_final: 0.8034 (tm-30) REVERT: D 655 LYS cc_start: 0.8370 (pptt) cc_final: 0.8101 (pptt) REVERT: E 104 MET cc_start: 0.9148 (ttt) cc_final: 0.8881 (tpp) REVERT: E 150 MET cc_start: 0.8430 (mmm) cc_final: 0.8128 (mmt) REVERT: E 256 SER cc_start: 0.9398 (p) cc_final: 0.9187 (m) REVERT: F 607 ASN cc_start: 0.8840 (p0) cc_final: 0.8274 (p0) REVERT: F 629 LEU cc_start: 0.8882 (tp) cc_final: 0.8643 (mp) REVERT: F 634 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8112 (mm-30) REVERT: F 648 GLU cc_start: 0.8479 (tp30) cc_final: 0.8234 (tp30) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2577 time to fit residues: 114.0986 Evaluate side-chains 239 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16072 Z= 0.221 Angle : 0.613 15.400 21852 Z= 0.308 Chirality : 0.046 0.392 2773 Planarity : 0.004 0.052 2679 Dihedral : 6.874 56.267 3805 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.21), residues: 1678 helix: 1.09 (0.27), residues: 422 sheet: 0.69 (0.24), residues: 440 loop : -0.30 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 69 HIS 0.004 0.001 HIS E 249 PHE 0.017 0.002 PHE C 210 TYR 0.017 0.002 TYR E 173 ARG 0.007 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9071 (mtp) cc_final: 0.8868 (mtm) REVERT: A 256 SER cc_start: 0.9398 (p) cc_final: 0.9084 (m) REVERT: A 315 GLN cc_start: 0.8794 (mp10) cc_final: 0.8524 (mp10) REVERT: B 535 MET cc_start: 0.8189 (mpp) cc_final: 0.7532 (mmm) REVERT: B 588 ARG cc_start: 0.8352 (ttt180) cc_final: 0.8091 (ttt180) REVERT: B 599 SER cc_start: 0.9044 (p) cc_final: 0.8382 (t) REVERT: B 602 LEU cc_start: 0.8636 (mt) cc_final: 0.8408 (pt) REVERT: B 634 GLU cc_start: 0.8656 (pt0) cc_final: 0.7766 (pp20) REVERT: B 641 ILE cc_start: 0.8316 (mp) cc_final: 0.7679 (tp) REVERT: C 38 VAL cc_start: 0.8474 (t) cc_final: 0.8219 (t) REVERT: C 114 GLN cc_start: 0.8845 (tp40) cc_final: 0.7849 (tm-30) REVERT: C 199 SER cc_start: 0.9288 (p) cc_final: 0.8884 (m) REVERT: C 258 GLN cc_start: 0.8817 (mt0) cc_final: 0.8453 (tt0) REVERT: C 414 ILE cc_start: 0.9365 (mm) cc_final: 0.9050 (tp) REVERT: D 535 MET cc_start: 0.8111 (ptp) cc_final: 0.7857 (ptp) REVERT: D 588 ARG cc_start: 0.9070 (tmm-80) cc_final: 0.8788 (ttp80) REVERT: D 615 SER cc_start: 0.8524 (t) cc_final: 0.8235 (m) REVERT: D 648 GLU cc_start: 0.8346 (tp30) cc_final: 0.8073 (tp30) REVERT: E 104 MET cc_start: 0.9193 (ttt) cc_final: 0.8914 (tpp) REVERT: E 150 MET cc_start: 0.8411 (mmm) cc_final: 0.8140 (mmt) REVERT: E 308 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8477 (mtm180) REVERT: E 500 ARG cc_start: 0.5985 (mtt180) cc_final: 0.4966 (pmt170) REVERT: F 530 MET cc_start: 0.8858 (mpp) cc_final: 0.8652 (mmt) REVERT: F 607 ASN cc_start: 0.8861 (p0) cc_final: 0.8295 (p0) REVERT: F 629 LEU cc_start: 0.8943 (tp) cc_final: 0.8550 (tp) REVERT: F 630 GLN cc_start: 0.8458 (tt0) cc_final: 0.8217 (tt0) REVERT: F 634 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8089 (mm-30) REVERT: F 648 GLU cc_start: 0.8449 (tp30) cc_final: 0.8235 (tp30) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2636 time to fit residues: 113.2470 Evaluate side-chains 236 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 99 ASN E 195 ASN E 249 HIS E 425 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16072 Z= 0.209 Angle : 0.617 15.291 21852 Z= 0.311 Chirality : 0.047 0.508 2773 Planarity : 0.004 0.042 2679 Dihedral : 6.796 56.152 3805 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.45 (0.21), residues: 1678 helix: 1.12 (0.27), residues: 420 sheet: 0.74 (0.24), residues: 450 loop : -0.33 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 610 HIS 0.004 0.001 HIS E 249 PHE 0.012 0.002 PHE A 468 TYR 0.019 0.002 TYR A 173 ARG 0.007 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8958 (tpp) cc_final: 0.8114 (tpp) REVERT: A 150 MET cc_start: 0.9147 (mtp) cc_final: 0.8924 (mtm) REVERT: A 256 SER cc_start: 0.9376 (p) cc_final: 0.9045 (m) REVERT: A 315 GLN cc_start: 0.8842 (mp10) cc_final: 0.8575 (mp10) REVERT: B 535 MET cc_start: 0.8165 (mpp) cc_final: 0.7490 (mmm) REVERT: B 588 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7397 (ttm-80) REVERT: B 599 SER cc_start: 0.9092 (p) cc_final: 0.8431 (t) REVERT: B 601 LYS cc_start: 0.8971 (ptpt) cc_final: 0.8496 (tptp) REVERT: B 602 LEU cc_start: 0.8688 (mt) cc_final: 0.8398 (pt) REVERT: B 634 GLU cc_start: 0.8658 (pt0) cc_final: 0.7802 (pp20) REVERT: B 641 ILE cc_start: 0.8416 (mp) cc_final: 0.7774 (tp) REVERT: C 38 VAL cc_start: 0.8596 (t) cc_final: 0.8322 (t) REVERT: C 39 TYR cc_start: 0.8910 (m-80) cc_final: 0.8616 (m-80) REVERT: C 114 GLN cc_start: 0.8885 (tp40) cc_final: 0.7903 (tm-30) REVERT: C 199 SER cc_start: 0.9310 (p) cc_final: 0.8909 (m) REVERT: C 414 ILE cc_start: 0.9361 (mm) cc_final: 0.9050 (tp) REVERT: C 490 LYS cc_start: 0.8745 (tttm) cc_final: 0.8360 (ttmt) REVERT: D 535 MET cc_start: 0.8136 (ptp) cc_final: 0.7860 (ptp) REVERT: D 577 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 610 TRP cc_start: 0.7467 (t60) cc_final: 0.7085 (t60) REVERT: E 104 MET cc_start: 0.9157 (ttt) cc_final: 0.8850 (tpp) REVERT: E 150 MET cc_start: 0.8391 (mmm) cc_final: 0.8142 (mmt) REVERT: E 308 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8512 (mtm180) REVERT: E 500 ARG cc_start: 0.5987 (mtt180) cc_final: 0.4995 (pmt170) REVERT: F 607 ASN cc_start: 0.8886 (p0) cc_final: 0.8286 (p0) REVERT: F 629 LEU cc_start: 0.8929 (tp) cc_final: 0.8686 (mp) REVERT: F 634 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8035 (mm-30) REVERT: F 648 GLU cc_start: 0.8446 (tp30) cc_final: 0.8219 (tp30) REVERT: F 652 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8293 (tt0) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2620 time to fit residues: 113.4380 Evaluate side-chains 234 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 99 ASN E 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16072 Z= 0.256 Angle : 0.668 15.157 21852 Z= 0.337 Chirality : 0.048 0.496 2773 Planarity : 0.004 0.041 2679 Dihedral : 6.939 56.486 3805 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.15 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.21), residues: 1678 helix: 0.95 (0.27), residues: 420 sheet: 0.63 (0.24), residues: 459 loop : -0.38 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 614 HIS 0.008 0.001 HIS A 216 PHE 0.012 0.002 PHE C 383 TYR 0.019 0.002 TYR A 173 ARG 0.006 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9020 (ttm) cc_final: 0.8480 (tpp) REVERT: A 217 TYR cc_start: 0.8721 (m-10) cc_final: 0.7451 (m-10) REVERT: A 256 SER cc_start: 0.9389 (p) cc_final: 0.9040 (m) REVERT: A 462 ASN cc_start: 0.7731 (t0) cc_final: 0.7487 (t0) REVERT: B 535 MET cc_start: 0.8157 (mpp) cc_final: 0.7503 (mmm) REVERT: B 588 ARG cc_start: 0.8377 (ttt180) cc_final: 0.8149 (ttt180) REVERT: B 599 SER cc_start: 0.9096 (p) cc_final: 0.8516 (t) REVERT: B 602 LEU cc_start: 0.8699 (mt) cc_final: 0.8431 (pt) REVERT: B 634 GLU cc_start: 0.8641 (pt0) cc_final: 0.7797 (pp20) REVERT: B 641 ILE cc_start: 0.8353 (mp) cc_final: 0.7724 (tp) REVERT: C 39 TYR cc_start: 0.8874 (m-80) cc_final: 0.8619 (m-80) REVERT: C 114 GLN cc_start: 0.8888 (tp40) cc_final: 0.7884 (tm-30) REVERT: C 199 SER cc_start: 0.9319 (p) cc_final: 0.8935 (m) REVERT: C 414 ILE cc_start: 0.9397 (mm) cc_final: 0.9067 (tp) REVERT: D 535 MET cc_start: 0.8192 (ptp) cc_final: 0.7918 (ptp) REVERT: D 577 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 606 THR cc_start: 0.8804 (p) cc_final: 0.8538 (p) REVERT: E 104 MET cc_start: 0.9164 (ttt) cc_final: 0.8874 (tpp) REVERT: E 150 MET cc_start: 0.8395 (mmm) cc_final: 0.8172 (mmt) REVERT: E 161 MET cc_start: 0.9157 (tpp) cc_final: 0.8430 (ttm) REVERT: E 308 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8575 (mtm180) REVERT: E 500 ARG cc_start: 0.5917 (mtt180) cc_final: 0.5032 (pmt170) REVERT: F 607 ASN cc_start: 0.8940 (p0) cc_final: 0.8342 (p0) REVERT: F 629 LEU cc_start: 0.8987 (tp) cc_final: 0.8310 (pp) REVERT: F 634 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8087 (mm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2749 time to fit residues: 110.0077 Evaluate side-chains 220 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 99 ASN E 195 ASN E 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16072 Z= 0.281 Angle : 0.672 15.125 21852 Z= 0.339 Chirality : 0.048 0.501 2773 Planarity : 0.004 0.050 2679 Dihedral : 7.077 58.987 3805 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1678 helix: 0.83 (0.26), residues: 421 sheet: 0.55 (0.24), residues: 450 loop : -0.50 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP D 614 HIS 0.006 0.001 HIS D 564 PHE 0.017 0.002 PHE C 383 TYR 0.020 0.002 TYR A 173 ARG 0.009 0.001 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9048 (ttm) cc_final: 0.8325 (tpp) REVERT: A 217 TYR cc_start: 0.8767 (m-10) cc_final: 0.7476 (m-80) REVERT: A 256 SER cc_start: 0.9403 (p) cc_final: 0.9083 (m) REVERT: B 535 MET cc_start: 0.8201 (mpp) cc_final: 0.7567 (mmt) REVERT: B 588 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8188 (ttt180) REVERT: B 599 SER cc_start: 0.9102 (p) cc_final: 0.8550 (t) REVERT: B 602 LEU cc_start: 0.8601 (mt) cc_final: 0.8365 (pt) REVERT: B 634 GLU cc_start: 0.8459 (pt0) cc_final: 0.7655 (pp20) REVERT: B 641 ILE cc_start: 0.8386 (mp) cc_final: 0.7747 (tp) REVERT: C 39 TYR cc_start: 0.8860 (m-80) cc_final: 0.8636 (m-80) REVERT: C 114 GLN cc_start: 0.8919 (tp40) cc_final: 0.7896 (tm-30) REVERT: C 199 SER cc_start: 0.9259 (p) cc_final: 0.8876 (m) REVERT: C 414 ILE cc_start: 0.9420 (mm) cc_final: 0.9108 (tp) REVERT: D 535 MET cc_start: 0.8118 (ptp) cc_final: 0.7894 (ptp) REVERT: D 577 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8075 (tm-30) REVERT: E 150 MET cc_start: 0.8324 (mmm) cc_final: 0.8119 (mmt) REVERT: E 161 MET cc_start: 0.9162 (tpp) cc_final: 0.8479 (ttm) REVERT: E 500 ARG cc_start: 0.5939 (mtt180) cc_final: 0.5070 (pmt170) REVERT: F 607 ASN cc_start: 0.8985 (p0) cc_final: 0.8532 (p0) REVERT: F 626 MET cc_start: 0.7582 (ttm) cc_final: 0.7309 (ttm) REVERT: F 629 LEU cc_start: 0.8796 (tp) cc_final: 0.8378 (tp) REVERT: F 634 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8077 (mm-30) REVERT: F 654 GLU cc_start: 0.9062 (tp30) cc_final: 0.8660 (tp30) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.2756 time to fit residues: 112.0722 Evaluate side-chains 223 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 195 ASN E 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088035 restraints weight = 35994.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.090330 restraints weight = 22129.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091903 restraints weight = 15879.533| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16072 Z= 0.214 Angle : 0.655 16.404 21852 Z= 0.330 Chirality : 0.047 0.473 2773 Planarity : 0.004 0.049 2679 Dihedral : 6.928 59.383 3805 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.97 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1678 helix: 0.93 (0.27), residues: 419 sheet: 0.49 (0.24), residues: 456 loop : -0.50 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 610 HIS 0.009 0.001 HIS D 564 PHE 0.015 0.002 PHE C 210 TYR 0.019 0.002 TYR A 217 ARG 0.007 0.001 ARG D 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.03 seconds wall clock time: 58 minutes 9.21 seconds (3489.21 seconds total)