Starting phenix.real_space_refine on Thu Mar 21 05:47:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb4_24969/03_2024/7sb4_24969_updated.pdb" } resolution = 4.7 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= 0.005 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 189 5.16 5 C 18618 2.51 5 N 4778 2.21 5 O 5746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 942": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 811": "OE1" <-> "OE2" Residue "B TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29331 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 9151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9151 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "C" Number of atoms: 9134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9134 Classifications: {'peptide': 1173} Link IDs: {'PTRANS': 50, 'TRANS': 1122} Chain breaks: 6 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9178 Classifications: {'peptide': 1180} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "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: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 172 Unusual residues: {'8Z9': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'8Z9': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'8Z9': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.24, per 1000 atoms: 0.52 Number of scatterers: 29331 At special positions: 0 Unit cell: (150.38, 164.8, 161.71, 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 189 16.00 O 5746 8.00 N 4778 7.00 C 18618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.02 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.11 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.08 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.05 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.02 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.04 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.02 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 173 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 260 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 308 " distance=2.06 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.09 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.04 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.05 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.07 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.04 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 747 " - pdb=" SG CYS C 756 " distance=1.73 Simple disulfide: pdb=" SG CYS C 825 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C 830 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 937 " - pdb=" SG CYS C 948 " distance=2.09 Simple disulfide: pdb=" SG CYS C1125 " - pdb=" SG CYS C1136 " distance=2.02 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1220 " distance=2.02 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.02 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.05 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.05 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.04 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.04 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.07 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.04 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " 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 P 1 " - " NAG P 2 " NAG-ASN " NAG A1401 " - " ASN A 137 " " NAG A1402 " - " ASN A 212 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A1193 " " NAG A1407 " - " ASN A 675 " " NAG A1408 " - " ASN A 695 " " NAG A1409 " - " ASN A 648 " " NAG A1410 " - " ASN A 449 " " NAG A1411 " - " ASN A1223 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 449 " " NAG B1403 " - " ASN B 713 " " NAG B1404 " - " ASN B 787 " " NAG B1405 " - " ASN B 936 " " NAG B1406 " - " ASN B1193 " " NAG B1407 " - " ASN B 675 " " NAG B1408 " - " ASN B 695 " " NAG B1409 " - " ASN B 648 " " NAG B1410 " - " ASN B1223 " " NAG C1401 " - " ASN C 212 " " NAG C1402 " - " ASN C 449 " " NAG C1403 " - " ASN C 713 " " NAG C1404 " - " ASN C 787 " " NAG C1405 " - " ASN C 936 " " NAG C1406 " - " ASN C 675 " " NAG C1407 " - " ASN C 695 " " NAG C1408 " - " ASN C 648 " " NAG C1409 " - " ASN C 371 " " NAG C1410 " - " ASN C1223 " " NAG D 1 " - " ASN A 738 " " NAG E 1 " - " ASN A 206 " " NAG F 1 " - " ASN A 371 " " NAG G 1 " - " ASN C 137 " " NAG I 1 " - " ASN C 738 " " NAG J 1 " - " ASN C1193 " " NAG K 1 " - " ASN C 206 " " NAG M 1 " - " ASN B 137 " " NAG N 1 " - " ASN B 371 " " NAG O 1 " - " ASN B 738 " " NAG P 1 " - " ASN B 206 " Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 4.5 seconds 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 54 sheets defined 22.8% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.48 Creating SS restraints... Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 417 No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 873 removed outlier: 4.231A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 914 through 922 removed outlier: 4.010A pdb=" N LYS A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 946 through 952 Processing helix chain 'A' and resid 964 through 979 removed outlier: 3.736A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1030 Processing helix chain 'A' and resid 1036 through 1060 removed outlier: 3.671A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 3.910A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 372 through 378 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 414 through 417 Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 539 through 541 No H-bonds generated for 'chain 'C' and resid 539 through 541' Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 825 through 827 No H-bonds generated for 'chain 'C' and resid 825 through 827' Processing helix chain 'C' and resid 834 through 873 removed outlier: 3.691A pdb=" N VAL C 841 " --> pdb=" O LYS C 837 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER C 845 " --> pdb=" O VAL C 841 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE C 846 " --> pdb=" O GLU C 842 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS C 847 " --> pdb=" O TYR C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 883 removed outlier: 3.549A pdb=" N LYS C 883 " --> pdb=" O THR C 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 880 through 883' Processing helix chain 'C' and resid 914 through 922 Processing helix chain 'C' and resid 927 through 933 Processing helix chain 'C' and resid 946 through 953 Processing helix chain 'C' and resid 964 through 979 Processing helix chain 'C' and resid 991 through 1002 Processing helix chain 'C' and resid 1006 through 1011 Processing helix chain 'C' and resid 1013 through 1029 Processing helix chain 'C' and resid 1036 through 1060 removed outlier: 4.010A pdb=" N LEU C1059 " --> pdb=" O LEU C1055 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1076 Processing helix chain 'C' and resid 1079 through 1125 removed outlier: 5.002A pdb=" N ALA C1084 " --> pdb=" O PRO C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1213 No H-bonds generated for 'chain 'C' and resid 1211 through 1213' Processing helix chain 'B' and resid 92 through 95 Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 378 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 414 through 417 No H-bonds generated for 'chain 'B' and resid 414 through 417' Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 825 through 829 Processing helix chain 'B' and resid 834 through 873 removed outlier: 3.751A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 883 Processing helix chain 'B' and resid 914 through 921 Processing helix chain 'B' and resid 927 through 933 Processing helix chain 'B' and resid 936 through 938 No H-bonds generated for 'chain 'B' and resid 936 through 938' Processing helix chain 'B' and resid 946 through 952 Processing helix chain 'B' and resid 964 through 979 Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1006 through 1011 Processing helix chain 'B' and resid 1013 through 1029 Processing helix chain 'B' and resid 1036 through 1059 Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1124 removed outlier: 3.800A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'A' and resid 64 through 73 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 102 Processing sheet with id= D, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.595A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= F, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= G, first strand: chain 'A' and resid 331 through 335 removed outlier: 5.824A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.195A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.596A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= K, first strand: chain 'A' and resid 797 through 802 Processing sheet with id= L, first strand: chain 'A' and resid 805 through 815 removed outlier: 3.522A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 820 through 823 removed outlier: 3.861A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1181 through 1184 Processing sheet with id= O, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 4.219A pdb=" N GLY A1200 " --> pdb=" O TYR A1205 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A1205 " --> pdb=" O GLY A1200 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 749 through 752 removed outlier: 4.229A pdb=" N LEU A 749 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 64 through 73 removed outlier: 3.607A pdb=" N ASN C 294 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 272 through 276 removed outlier: 5.273A pdb=" N PHE C 231 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE C 240 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 114 through 118 Processing sheet with id= T, first strand: chain 'C' and resid 252 through 255 Processing sheet with id= U, first strand: chain 'C' and resid 318 through 321 Processing sheet with id= V, first strand: chain 'C' and resid 331 through 335 removed outlier: 3.642A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 676 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU C 659 " --> pdb=" O TYR C 667 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 353 through 355 removed outlier: 5.987A pdb=" N SER C 451 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'C' and resid 361 through 365 removed outlier: 6.796A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 484 through 488 Processing sheet with id= Z, first strand: chain 'C' and resid 755 through 759 Processing sheet with id= AA, first strand: chain 'C' and resid 796 through 802 Processing sheet with id= AB, first strand: chain 'C' and resid 805 through 815 removed outlier: 3.542A pdb=" N ILE C1143 " --> pdb=" O PHE C1158 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR C1160 " --> pdb=" O HIS C1141 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS C1141 " --> pdb=" O TYR C1160 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 820 through 823 removed outlier: 3.949A pdb=" N LYS C 820 " --> pdb=" O LEU C 958 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 1225 through 1227 Processing sheet with id= AE, first strand: chain 'C' and resid 1187 through 1192 Processing sheet with id= AF, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AG, first strand: chain 'B' and resid 64 through 73 removed outlier: 3.604A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.407A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= AJ, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= AK, first strand: chain 'B' and resid 177 through 179 No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= AM, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.581A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 353 through 355 removed outlier: 5.984A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.549A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AQ, first strand: chain 'B' and resid 773 through 777 removed outlier: 6.329A pdb=" N VAL B 757 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR B 750 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 805 through 815 removed outlier: 3.607A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.044A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= AU, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id= AV, first strand: chain 'B' and resid 797 through 804 removed outlier: 6.450A pdb=" N LYS B1164 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 20 through 23 Processing sheet with id= AX, first strand: chain 'H' and resid 35 through 39 Processing sheet with id= AY, first strand: chain 'H' and resid 95 through 97 Processing sheet with id= AZ, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.566A pdb=" N UNK L 22 " --> pdb=" O UNK L 5 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'L' and resid 79 through 85 removed outlier: 3.521A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 58 through 61 1019 hydrogen bonds defined for protein. 2844 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: 13.19 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6882 1.32 - 1.47: 10544 1.47 - 1.62: 12288 1.62 - 1.77: 32 1.77 - 1.92: 216 Bond restraints: 29962 Sorted by residual: bond pdb=" CB HIS C 483 " pdb=" CG HIS C 483 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" CB HIS C 219 " pdb=" CG HIS C 219 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.56e+01 bond pdb=" CB ASN A1213 " pdb=" CG ASN A1213 " ideal model delta sigma weight residual 1.516 1.373 0.143 2.50e-02 1.60e+03 3.28e+01 bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 2.99e+01 bond pdb=" N PRO B 474 " pdb=" CD PRO B 474 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.65e+01 ... (remaining 29957 not shown) Histogram of bond angle deviations from ideal: 96.54 - 104.05: 433 104.05 - 111.57: 12496 111.57 - 119.08: 11871 119.08 - 126.60: 15739 126.60 - 134.11: 259 Bond angle restraints: 40798 Sorted by residual: angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.03 129.06 -9.03 9.90e-01 1.02e+00 8.33e+01 angle pdb=" C PRO C 959 " pdb=" N PRO C 960 " pdb=" CA PRO C 960 " ideal model delta sigma weight residual 120.21 128.75 -8.54 9.60e-01 1.09e+00 7.92e+01 angle pdb=" N THR B 577 " pdb=" CA THR B 577 " pdb=" C THR B 577 " ideal model delta sigma weight residual 109.24 96.54 12.70 1.51e+00 4.39e-01 7.08e+01 angle pdb=" C PRO A 37 " pdb=" N PRO A 38 " pdb=" CA PRO A 38 " ideal model delta sigma weight residual 118.97 127.64 -8.67 1.04e+00 9.25e-01 6.96e+01 angle pdb=" C ALA C1227 " pdb=" N PRO C1228 " pdb=" CA PRO C1228 " ideal model delta sigma weight residual 119.56 128.04 -8.48 1.02e+00 9.61e-01 6.92e+01 ... (remaining 40793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 18338 34.94 - 69.88: 191 69.88 - 104.81: 34 104.81 - 139.75: 6 139.75 - 174.69: 2 Dihedral angle restraints: 18571 sinusoidal: 7634 harmonic: 10937 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -141.84 55.84 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS C 535 " pdb=" SG CYS C 535 " pdb=" SG CYS C 548 " pdb=" CB CYS C 548 " ideal model delta sinusoidal sigma weight residual 93.00 147.45 -54.45 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 683 " pdb=" CB CYS A 683 " ideal model delta sinusoidal sigma weight residual -86.00 -136.81 50.81 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 18568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.964: 4788 0.964 - 1.928: 1 1.928 - 2.891: 0 2.891 - 3.855: 0 3.855 - 4.819: 1 Chirality restraints: 4790 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.42 -4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 ... (remaining 4787 not shown) Planarity restraints: 5248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1404 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1402 " 0.327 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG A1402 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1402 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A1402 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG A1402 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.312 2.00e-02 2.50e+03 2.65e-01 8.78e+02 pdb=" C7 NAG M 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.049 2.00e-02 2.50e+03 ... (remaining 5245 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6274 2.77 - 3.31: 28492 3.31 - 3.84: 50818 3.84 - 4.37: 62343 4.37 - 4.90: 98631 Nonbonded interactions: 246558 Sorted by model distance: nonbonded pdb=" O3 NAG M 2 " pdb=" O7 NAG M 2 " model vdw 2.242 2.440 nonbonded pdb=" N THR B 577 " pdb=" O THR B 577 " model vdw 2.361 2.496 nonbonded pdb=" N VAL C 136 " pdb=" O VAL C 136 " model vdw 2.364 2.496 nonbonded pdb=" N VAL B 136 " pdb=" O VAL B 136 " model vdw 2.384 2.496 nonbonded pdb=" O SER C 41 " pdb=" OG SER C 41 " model vdw 2.385 2.440 ... (remaining 246553 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 15 through 33 or resid 38 through 473 or resid 481 through \ 901 or resid 910 through 1232 or resid 1401 through 1410)) selection = (chain 'B' and (resid 15 through 33 or resid 38 through 150 or resid 158 through \ 473 or resid 481 through 504 or resid 518 through 762 or resid 772 through 901 \ or resid 910 through 1232 or resid 1401 through 1410)) selection = (chain 'C' and (resid 15 through 504 or resid 518 through 762 or resid 772 throu \ gh 1232 or resid 1401 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 17 through 115) selection = chain 'L' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 9.730 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 79.220 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.320 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 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 : 0.020 0.143 29962 Z= 1.266 Angle : 1.788 14.379 40798 Z= 1.193 Chirality : 0.136 4.819 4790 Planarity : 0.015 0.302 5206 Dihedral : 11.157 174.688 11370 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.17 % 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: 0.54 (0.13), residues: 3491 helix: 0.23 (0.16), residues: 831 sheet: 0.90 (0.18), residues: 734 loop : 0.34 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.010 TRP B 586 HIS 0.022 0.003 HIS B 219 PHE 0.054 0.006 PHE B 464 TYR 0.086 0.009 TYR A 79 ARG 0.014 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 812 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.7437 (tt) cc_final: 0.7013 (tt) REVERT: A 104 ILE cc_start: 0.8238 (mm) cc_final: 0.7920 (pt) REVERT: A 129 ILE cc_start: 0.8159 (pt) cc_final: 0.7783 (pt) REVERT: A 145 GLN cc_start: 0.7394 (pt0) cc_final: 0.7191 (tt0) REVERT: A 165 VAL cc_start: 0.6597 (t) cc_final: 0.6368 (p) REVERT: A 263 ARG cc_start: 0.7104 (mmt180) cc_final: 0.6705 (mtm180) REVERT: A 296 VAL cc_start: 0.5529 (t) cc_final: 0.4550 (t) REVERT: A 332 ASP cc_start: 0.6669 (m-30) cc_final: 0.6352 (m-30) REVERT: A 361 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6215 (mt-10) REVERT: A 375 LEU cc_start: 0.7848 (tp) cc_final: 0.7575 (mp) REVERT: A 376 MET cc_start: 0.7476 (mtm) cc_final: 0.5618 (ptp) REVERT: A 397 MET cc_start: 0.8095 (ttm) cc_final: 0.7866 (ttp) REVERT: A 433 ASP cc_start: 0.8458 (t0) cc_final: 0.8060 (t0) REVERT: A 625 ILE cc_start: 0.8395 (mt) cc_final: 0.8093 (tp) REVERT: A 663 ASN cc_start: 0.6674 (m-40) cc_final: 0.6330 (m-40) REVERT: A 667 TYR cc_start: 0.5206 (p90) cc_final: 0.4956 (p90) REVERT: A 734 VAL cc_start: 0.7743 (t) cc_final: 0.7362 (p) REVERT: A 807 ILE cc_start: 0.8276 (mt) cc_final: 0.7966 (tp) REVERT: A 849 ASN cc_start: 0.7881 (m-40) cc_final: 0.7355 (m-40) REVERT: A 873 MET cc_start: 0.7130 (ppp) cc_final: 0.6658 (ppp) REVERT: A 892 ASP cc_start: 0.5519 (t0) cc_final: 0.4979 (t0) REVERT: A 916 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 943 ILE cc_start: 0.5931 (mm) cc_final: 0.5686 (tp) REVERT: A 970 TYR cc_start: 0.8147 (m-80) cc_final: 0.7546 (m-80) REVERT: A 1010 SER cc_start: 0.7565 (t) cc_final: 0.6777 (m) REVERT: A 1061 ASN cc_start: 0.7876 (m110) cc_final: 0.7360 (m110) REVERT: A 1081 GLU cc_start: 0.7035 (tp30) cc_final: 0.6281 (mp0) REVERT: A 1089 LEU cc_start: 0.8186 (mt) cc_final: 0.7846 (tp) REVERT: A 1134 ASN cc_start: 0.8387 (m-40) cc_final: 0.8026 (m110) REVERT: A 1230 VAL cc_start: 0.7040 (t) cc_final: 0.6147 (t) REVERT: C 16 ILE cc_start: 0.8355 (mm) cc_final: 0.7876 (mm) REVERT: C 45 VAL cc_start: 0.6960 (t) cc_final: 0.6621 (t) REVERT: C 60 VAL cc_start: 0.7366 (p) cc_final: 0.6832 (p) REVERT: C 89 LYS cc_start: 0.5830 (mmtm) cc_final: 0.5511 (pptt) REVERT: C 125 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7677 (pm20) REVERT: C 166 SER cc_start: 0.8380 (p) cc_final: 0.7984 (m) REVERT: C 170 TYR cc_start: 0.5756 (p90) cc_final: 0.5312 (p90) REVERT: C 177 HIS cc_start: 0.7729 (m90) cc_final: 0.6955 (m90) REVERT: C 192 TRP cc_start: 0.6996 (p-90) cc_final: 0.6395 (p-90) REVERT: C 307 LYS cc_start: 0.7345 (mttt) cc_final: 0.7113 (mttt) REVERT: C 321 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 346 GLU cc_start: 0.7205 (mp0) cc_final: 0.6496 (pp20) REVERT: C 382 ASP cc_start: 0.8521 (m-30) cc_final: 0.8071 (t0) REVERT: C 397 MET cc_start: 0.6334 (ttm) cc_final: 0.5919 (ttm) REVERT: C 437 THR cc_start: 0.7747 (m) cc_final: 0.7436 (t) REVERT: C 440 GLN cc_start: 0.7670 (mp10) cc_final: 0.7433 (mp10) REVERT: C 445 LEU cc_start: 0.6810 (mt) cc_final: 0.6390 (mt) REVERT: C 450 VAL cc_start: 0.8062 (t) cc_final: 0.7798 (m) REVERT: C 546 TYR cc_start: 0.7030 (m-80) cc_final: 0.6436 (p90) REVERT: C 602 ASN cc_start: 0.7282 (t0) cc_final: 0.6536 (t0) REVERT: C 626 LYS cc_start: 0.8180 (mttp) cc_final: 0.7536 (mmmt) REVERT: C 679 MET cc_start: 0.7979 (mmm) cc_final: 0.7438 (mmm) REVERT: C 724 ASN cc_start: 0.5806 (m-40) cc_final: 0.5396 (m110) REVERT: C 824 ASP cc_start: 0.8136 (t0) cc_final: 0.7702 (t0) REVERT: C 881 LYS cc_start: 0.7738 (mttm) cc_final: 0.6927 (mtmt) REVERT: C 882 LEU cc_start: 0.8438 (mt) cc_final: 0.8211 (mp) REVERT: C 883 LYS cc_start: 0.6895 (mmmt) cc_final: 0.6618 (tppt) REVERT: C 965 ASN cc_start: 0.7184 (m-40) cc_final: 0.6896 (m110) REVERT: C 989 VAL cc_start: 0.7949 (t) cc_final: 0.6544 (t) REVERT: C 994 ASN cc_start: 0.8373 (t0) cc_final: 0.8067 (m-40) REVERT: C 1002 LEU cc_start: 0.7505 (mt) cc_final: 0.7248 (tp) REVERT: C 1113 PHE cc_start: 0.7656 (t80) cc_final: 0.7164 (t80) REVERT: C 1133 ILE cc_start: 0.7848 (mm) cc_final: 0.7204 (mm) REVERT: C 1165 TYR cc_start: 0.6403 (m-80) cc_final: 0.6153 (m-80) REVERT: C 1179 ASP cc_start: 0.6891 (m-30) cc_final: 0.6524 (t0) REVERT: C 1197 MET cc_start: 0.5926 (mtp) cc_final: 0.5589 (mtt) REVERT: B 82 MET cc_start: 0.7144 (mmm) cc_final: 0.6465 (tpp) REVERT: B 88 ASP cc_start: 0.8352 (t0) cc_final: 0.8084 (t70) REVERT: B 164 GLU cc_start: 0.5740 (mt-10) cc_final: 0.5526 (pt0) REVERT: B 170 TYR cc_start: 0.5389 (m-80) cc_final: 0.5017 (m-80) REVERT: B 172 MET cc_start: 0.8282 (mtp) cc_final: 0.7870 (mtp) REVERT: B 209 TYR cc_start: 0.7372 (p90) cc_final: 0.7045 (p90) REVERT: B 217 TYR cc_start: 0.6448 (m-80) cc_final: 0.5908 (m-80) REVERT: B 299 MET cc_start: 0.7695 (mmm) cc_final: 0.6532 (ttp) REVERT: B 383 SER cc_start: 0.7192 (t) cc_final: 0.6468 (p) REVERT: B 452 VAL cc_start: 0.7306 (t) cc_final: 0.6808 (p) REVERT: B 485 VAL cc_start: 0.7097 (t) cc_final: 0.6859 (m) REVERT: B 554 LEU cc_start: 0.8483 (mt) cc_final: 0.8238 (mm) REVERT: B 589 ASP cc_start: 0.5980 (t0) cc_final: 0.5201 (m-30) REVERT: B 655 TRP cc_start: 0.5651 (p-90) cc_final: 0.5423 (p-90) REVERT: B 656 GLN cc_start: 0.7720 (mt0) cc_final: 0.6304 (mt0) REVERT: B 669 PHE cc_start: 0.7260 (t80) cc_final: 0.6784 (t80) REVERT: B 737 TYR cc_start: 0.7367 (t80) cc_final: 0.7098 (m-10) REVERT: B 798 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7299 (mm-30) REVERT: B 812 GLU cc_start: 0.7578 (tp30) cc_final: 0.6727 (mt-10) REVERT: B 853 ILE cc_start: 0.7337 (mt) cc_final: 0.6878 (mt) REVERT: B 874 ASN cc_start: 0.6720 (t0) cc_final: 0.6481 (t0) REVERT: B 881 LYS cc_start: 0.6830 (mttm) cc_final: 0.6430 (mttp) REVERT: B 892 ASP cc_start: 0.7659 (m-30) cc_final: 0.7085 (t0) REVERT: B 915 ILE cc_start: 0.8518 (mt) cc_final: 0.7905 (mt) REVERT: B 951 SER cc_start: 0.8946 (t) cc_final: 0.8646 (m) REVERT: B 998 ARG cc_start: 0.7639 (mmm160) cc_final: 0.6858 (tpp-160) REVERT: B 1005 THR cc_start: 0.7659 (m) cc_final: 0.7343 (p) REVERT: B 1135 PHE cc_start: 0.7383 (t80) cc_final: 0.6768 (t80) REVERT: B 1197 MET cc_start: 0.8535 (mtp) cc_final: 0.8317 (mmm) REVERT: B 1224 TYR cc_start: 0.6623 (m-10) cc_final: 0.6309 (m-10) outliers start: 0 outliers final: 0 residues processed: 812 average time/residue: 0.4027 time to fit residues: 516.7399 Evaluate side-chains 344 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 337 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 187 HIS A 344 ASN A 440 GLN A 705 ASN A 996 GLN C 105 ASN ** C 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 714 ASN C 724 ASN C 996 GLN C1028 GLN C1057 GLN C1058 GLN C1117 GLN C1138 ASN C1148 ASN B 421 ASN B 966 GLN B 994 ASN B1018 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 GLN B1091 ASN B1103 GLN ** B1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1147 GLN B1194 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29962 Z= 0.243 Angle : 0.731 13.868 40798 Z= 0.380 Chirality : 0.052 1.140 4790 Planarity : 0.004 0.043 5206 Dihedral : 8.953 162.819 5211 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.16 % Allowed : 1.99 % Favored : 97.85 % 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: 0.71 (0.14), residues: 3491 helix: 1.51 (0.18), residues: 809 sheet: 0.68 (0.18), residues: 726 loop : 0.02 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 360 HIS 0.007 0.001 HIS C 193 PHE 0.041 0.002 PHE C1113 TYR 0.028 0.002 TYR C 570 ARG 0.019 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 459 time to evaluate : 3.200 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: A 194 MET cc_start: 0.5862 (tpt) cc_final: 0.4709 (tmm) REVERT: A 248 MET cc_start: 0.7319 (mpp) cc_final: 0.6965 (mpp) REVERT: A 254 TYR cc_start: 0.6074 (t80) cc_final: 0.5609 (t80) REVERT: A 256 MET cc_start: 0.6679 (ptp) cc_final: 0.6309 (ptm) REVERT: A 307 LYS cc_start: 0.7477 (mttt) cc_final: 0.7201 (mtmt) REVERT: A 315 PRO cc_start: 0.8240 (Cg_endo) cc_final: 0.7845 (Cg_exo) REVERT: A 361 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6389 (mt-10) REVERT: A 433 ASP cc_start: 0.8634 (t0) cc_final: 0.8398 (t0) REVERT: A 625 ILE cc_start: 0.8404 (mt) cc_final: 0.8118 (tp) REVERT: A 659 LEU cc_start: 0.6848 (tp) cc_final: 0.6558 (tp) REVERT: A 667 TYR cc_start: 0.4361 (p90) cc_final: 0.3991 (p90) REVERT: A 810 MET cc_start: 0.7208 (mpp) cc_final: 0.6794 (mpp) REVERT: A 892 ASP cc_start: 0.5525 (t0) cc_final: 0.4889 (t0) REVERT: A 916 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 970 TYR cc_start: 0.8211 (m-80) cc_final: 0.7942 (m-80) REVERT: A 1107 ASP cc_start: 0.6893 (m-30) cc_final: 0.6457 (t70) REVERT: A 1138 ASN cc_start: 0.8129 (m-40) cc_final: 0.7289 (p0) REVERT: A 1217 MET cc_start: 0.7077 (ptp) cc_final: 0.6378 (ptp) REVERT: C 89 LYS cc_start: 0.5863 (mmtm) cc_final: 0.5565 (pptt) REVERT: C 125 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7580 (pm20) REVERT: C 166 SER cc_start: 0.8159 (p) cc_final: 0.7716 (p) REVERT: C 170 TYR cc_start: 0.5117 (p90) cc_final: 0.4630 (p90) REVERT: C 321 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8008 (mm-30) REVERT: C 346 GLU cc_start: 0.7185 (mp0) cc_final: 0.6501 (tm-30) REVERT: C 352 LYS cc_start: 0.8081 (pttt) cc_final: 0.7785 (mptt) REVERT: C 397 MET cc_start: 0.5904 (ttm) cc_final: 0.5414 (ttm) REVERT: C 492 PHE cc_start: 0.5955 (m-80) cc_final: 0.5636 (m-10) REVERT: C 546 TYR cc_start: 0.7093 (m-80) cc_final: 0.6531 (p90) REVERT: C 602 ASN cc_start: 0.7438 (t0) cc_final: 0.5457 (t0) REVERT: C 626 LYS cc_start: 0.7964 (mttp) cc_final: 0.7338 (mmmt) REVERT: C 646 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6239 (tp30) REVERT: C 724 ASN cc_start: 0.5812 (m110) cc_final: 0.4654 (m-40) REVERT: C 824 ASP cc_start: 0.8202 (t0) cc_final: 0.7795 (t0) REVERT: C 882 LEU cc_start: 0.8232 (mt) cc_final: 0.8010 (mt) REVERT: C 883 LYS cc_start: 0.6580 (mmmt) cc_final: 0.6270 (tppt) REVERT: C 994 ASN cc_start: 0.8274 (t0) cc_final: 0.8041 (m110) REVERT: C 1002 LEU cc_start: 0.7711 (mt) cc_final: 0.7456 (tp) REVERT: C 1005 THR cc_start: 0.7348 (t) cc_final: 0.6698 (p) REVERT: C 1197 MET cc_start: 0.6227 (mtp) cc_final: 0.5876 (mtt) REVERT: B 66 LEU cc_start: 0.6631 (mp) cc_final: 0.6328 (mp) REVERT: B 108 PHE cc_start: 0.6738 (t80) cc_final: 0.6524 (t80) REVERT: B 163 LEU cc_start: 0.8196 (tp) cc_final: 0.7916 (tp) REVERT: B 170 TYR cc_start: 0.5084 (m-80) cc_final: 0.4613 (m-80) REVERT: B 172 MET cc_start: 0.8396 (mtp) cc_final: 0.7720 (mtm) REVERT: B 194 MET cc_start: 0.4458 (ttm) cc_final: 0.3584 (mtp) REVERT: B 209 TYR cc_start: 0.7226 (p90) cc_final: 0.6760 (p90) REVERT: B 217 TYR cc_start: 0.6480 (m-80) cc_final: 0.5824 (m-80) REVERT: B 287 ASN cc_start: 0.6705 (t0) cc_final: 0.5970 (m-40) REVERT: B 383 SER cc_start: 0.6794 (t) cc_final: 0.6310 (p) REVERT: B 418 GLN cc_start: 0.5956 (tm-30) cc_final: 0.5483 (tm-30) REVERT: B 452 VAL cc_start: 0.7390 (t) cc_final: 0.7018 (p) REVERT: B 484 ASP cc_start: 0.6995 (t0) cc_final: 0.6741 (m-30) REVERT: B 589 ASP cc_start: 0.5764 (t0) cc_final: 0.5456 (t0) REVERT: B 669 PHE cc_start: 0.6886 (t80) cc_final: 0.6613 (t80) REVERT: B 798 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7224 (mm-30) REVERT: B 812 GLU cc_start: 0.7178 (tp30) cc_final: 0.6317 (mt-10) REVERT: B 846 PHE cc_start: 0.8349 (m-80) cc_final: 0.7859 (m-80) REVERT: B 862 ASP cc_start: 0.8479 (t0) cc_final: 0.8028 (t70) REVERT: B 874 ASN cc_start: 0.6623 (t0) cc_final: 0.6360 (t0) REVERT: B 882 LEU cc_start: 0.7748 (mt) cc_final: 0.7428 (mt) REVERT: B 892 ASP cc_start: 0.7672 (m-30) cc_final: 0.7250 (t0) REVERT: B 1005 THR cc_start: 0.7760 (m) cc_final: 0.7232 (p) REVERT: B 1135 PHE cc_start: 0.7539 (t80) cc_final: 0.7282 (t80) REVERT: B 1197 MET cc_start: 0.8807 (mtp) cc_final: 0.7985 (mmm) REVERT: B 1217 MET cc_start: 0.7087 (mpp) cc_final: 0.6727 (mpp) outliers start: 5 outliers final: 1 residues processed: 464 average time/residue: 0.3875 time to fit residues: 295.3798 Evaluate side-chains 267 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 365 optimal weight: 40.0000 chunk 301 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 171 ASN A 219 HIS A 426 GLN A 444 ASN A 641 GLN A 849 ASN A 996 GLN A1000 ASN A1012 ASN A1103 GLN C 193 HIS C 281 GLN ** C1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 150 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 HIS B 219 HIS B 281 GLN B1028 GLN B1058 GLN B1071 GLN B1091 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 29962 Z= 0.379 Angle : 0.824 11.711 40798 Z= 0.424 Chirality : 0.051 0.592 4790 Planarity : 0.006 0.054 5206 Dihedral : 8.155 101.541 5211 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 0.26 % Allowed : 3.45 % Favored : 96.29 % 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: -0.06 (0.13), residues: 3491 helix: 0.83 (0.17), residues: 823 sheet: 0.32 (0.18), residues: 728 loop : -0.52 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 586 HIS 0.008 0.002 HIS B 560 PHE 0.035 0.003 PHE A1063 TYR 0.039 0.003 TYR A 725 ARG 0.012 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 340 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ILE cc_start: 0.8071 (pt) cc_final: 0.7732 (pt) REVERT: A 194 MET cc_start: 0.6413 (tpt) cc_final: 0.5642 (tmm) REVERT: A 315 PRO cc_start: 0.8045 (Cg_endo) cc_final: 0.7777 (Cg_exo) REVERT: A 589 ASP cc_start: 0.6588 (m-30) cc_final: 0.5927 (p0) REVERT: A 625 ILE cc_start: 0.8439 (mt) cc_final: 0.7955 (tp) REVERT: A 810 MET cc_start: 0.7301 (mpp) cc_final: 0.7065 (mpp) REVERT: A 916 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 961 LEU cc_start: 0.7794 (tp) cc_final: 0.7455 (tp) REVERT: A 1138 ASN cc_start: 0.8427 (m-40) cc_final: 0.7513 (p0) REVERT: A 1197 MET cc_start: 0.4748 (mmm) cc_final: 0.4441 (mmm) REVERT: C 89 LYS cc_start: 0.6045 (mmtm) cc_final: 0.5689 (pptt) REVERT: C 125 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7553 (pm20) REVERT: C 248 MET cc_start: 0.8543 (ppp) cc_final: 0.8270 (tmm) REVERT: C 352 LYS cc_start: 0.8240 (pttt) cc_final: 0.7945 (mptt) REVERT: C 397 MET cc_start: 0.6178 (ttm) cc_final: 0.5815 (ttm) REVERT: C 467 ILE cc_start: 0.7327 (mm) cc_final: 0.6639 (mm) REVERT: C 538 ASP cc_start: 0.7107 (m-30) cc_final: 0.6239 (p0) REVERT: C 589 ASP cc_start: 0.8271 (t0) cc_final: 0.7559 (p0) REVERT: C 735 ASN cc_start: 0.7653 (m110) cc_final: 0.7243 (m110) REVERT: C 824 ASP cc_start: 0.8332 (t0) cc_final: 0.7981 (t0) REVERT: C 866 LEU cc_start: 0.7483 (mt) cc_final: 0.7134 (tt) REVERT: C 874 ASN cc_start: 0.8146 (t0) cc_final: 0.7897 (p0) REVERT: C 883 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6618 (tppt) REVERT: C 993 LEU cc_start: 0.7728 (mt) cc_final: 0.7350 (mp) REVERT: C 994 ASN cc_start: 0.8478 (t0) cc_final: 0.8127 (m110) REVERT: B 170 TYR cc_start: 0.4202 (m-80) cc_final: 0.3421 (m-80) REVERT: B 209 TYR cc_start: 0.7421 (p90) cc_final: 0.6879 (p90) REVERT: B 217 TYR cc_start: 0.6525 (m-80) cc_final: 0.5826 (m-80) REVERT: B 282 TYR cc_start: 0.5008 (m-80) cc_final: 0.4690 (m-80) REVERT: B 656 GLN cc_start: 0.8082 (mt0) cc_final: 0.7708 (mt0) REVERT: B 669 PHE cc_start: 0.7063 (t80) cc_final: 0.6689 (t80) REVERT: B 798 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7511 (mm-30) REVERT: B 862 ASP cc_start: 0.8307 (t0) cc_final: 0.7947 (t0) REVERT: B 874 ASN cc_start: 0.6982 (t0) cc_final: 0.6590 (t0) REVERT: B 892 ASP cc_start: 0.7483 (m-30) cc_final: 0.7125 (t0) REVERT: B 1005 THR cc_start: 0.7813 (m) cc_final: 0.7412 (p) REVERT: B 1053 ASN cc_start: 0.8667 (t0) cc_final: 0.8285 (m110) REVERT: B 1197 MET cc_start: 0.8739 (mtp) cc_final: 0.8126 (mpp) REVERT: B 1217 MET cc_start: 0.7234 (mpp) cc_final: 0.7015 (mpp) outliers start: 8 outliers final: 2 residues processed: 346 average time/residue: 0.3925 time to fit residues: 227.1106 Evaluate side-chains 216 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 30.0000 chunk 177 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 171 ASN A 598 ASN A 705 ASN A 809 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN A1061 ASN A1104 GLN C 653 ASN C 839 GLN ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29962 Z= 0.341 Angle : 0.740 17.052 40798 Z= 0.379 Chirality : 0.049 0.406 4790 Planarity : 0.005 0.066 5206 Dihedral : 7.869 102.047 5211 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.04 % Cbeta Deviations : 0.03 % 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: -0.29 (0.13), residues: 3491 helix: 0.86 (0.18), residues: 825 sheet: 0.15 (0.18), residues: 742 loop : -0.78 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 192 HIS 0.008 0.002 HIS B1157 PHE 0.023 0.002 PHE B 980 TYR 0.030 0.002 TYR A 667 ARG 0.006 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 293 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6543 (mtm180) cc_final: 0.6228 (mpt180) REVERT: A 194 MET cc_start: 0.6714 (tpt) cc_final: 0.5861 (tmm) REVERT: A 203 TYR cc_start: 0.6916 (t80) cc_final: 0.6605 (t80) REVERT: A 307 LYS cc_start: 0.7435 (mttt) cc_final: 0.7183 (mtmt) REVERT: A 315 PRO cc_start: 0.8067 (Cg_endo) cc_final: 0.7712 (Cg_exo) REVERT: A 599 ILE cc_start: 0.7239 (mt) cc_final: 0.7037 (mt) REVERT: A 625 ILE cc_start: 0.8620 (mt) cc_final: 0.8215 (tp) REVERT: A 729 TYR cc_start: 0.8091 (t80) cc_final: 0.7753 (t80) REVERT: A 809 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7427 (p0) REVERT: A 810 MET cc_start: 0.7208 (mpp) cc_final: 0.6925 (mpp) REVERT: A 916 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 961 LEU cc_start: 0.7659 (tp) cc_final: 0.7316 (tp) REVERT: A 1138 ASN cc_start: 0.8506 (m-40) cc_final: 0.7749 (p0) REVERT: A 1197 MET cc_start: 0.4721 (mmm) cc_final: 0.4479 (mmm) REVERT: C 54 TYR cc_start: 0.6521 (p90) cc_final: 0.6218 (p90) REVERT: C 60 VAL cc_start: 0.7064 (t) cc_final: 0.6776 (m) REVERT: C 89 LYS cc_start: 0.5736 (mmtm) cc_final: 0.5426 (pptt) REVERT: C 125 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7546 (pm20) REVERT: C 307 LYS cc_start: 0.7351 (tttt) cc_final: 0.7053 (tttm) REVERT: C 321 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 352 LYS cc_start: 0.8371 (pttt) cc_final: 0.8076 (mptt) REVERT: C 397 MET cc_start: 0.6139 (ttm) cc_final: 0.5390 (ttm) REVERT: C 698 GLU cc_start: 0.8213 (pp20) cc_final: 0.7969 (pp20) REVERT: C 735 ASN cc_start: 0.7722 (m110) cc_final: 0.7303 (m110) REVERT: C 866 LEU cc_start: 0.7443 (mt) cc_final: 0.7087 (tt) REVERT: C 993 LEU cc_start: 0.7394 (mt) cc_final: 0.7172 (mp) REVERT: C 994 ASN cc_start: 0.8468 (t0) cc_final: 0.8100 (m110) REVERT: B 82 MET cc_start: 0.7004 (mmp) cc_final: 0.6774 (tpp) REVERT: B 88 ASP cc_start: 0.7726 (t0) cc_final: 0.7261 (t0) REVERT: B 163 LEU cc_start: 0.8253 (tt) cc_final: 0.7831 (tp) REVERT: B 209 TYR cc_start: 0.7654 (p90) cc_final: 0.7020 (p90) REVERT: B 217 TYR cc_start: 0.6410 (m-80) cc_final: 0.5743 (m-80) REVERT: B 282 TYR cc_start: 0.4739 (m-80) cc_final: 0.4420 (m-80) REVERT: B 717 ILE cc_start: 0.7223 (mm) cc_final: 0.6983 (pt) REVERT: B 725 TYR cc_start: 0.6757 (p90) cc_final: 0.6357 (p90) REVERT: B 798 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7812 (tt0) REVERT: B 862 ASP cc_start: 0.8305 (t0) cc_final: 0.8009 (t0) REVERT: B 874 ASN cc_start: 0.7021 (t0) cc_final: 0.6747 (t0) REVERT: B 892 ASP cc_start: 0.7605 (m-30) cc_final: 0.7330 (t0) REVERT: B 1005 THR cc_start: 0.7778 (m) cc_final: 0.7364 (p) REVERT: B 1053 ASN cc_start: 0.8694 (t0) cc_final: 0.8280 (m110) REVERT: B 1058 GLN cc_start: 0.8271 (mm110) cc_final: 0.8035 (tp-100) REVERT: B 1107 ASP cc_start: 0.8179 (t0) cc_final: 0.7623 (t0) REVERT: B 1151 TYR cc_start: 0.6573 (m-80) cc_final: 0.6251 (m-80) REVERT: B 1197 MET cc_start: 0.8660 (mtp) cc_final: 0.8062 (mmm) REVERT: B 1217 MET cc_start: 0.6950 (mpp) cc_final: 0.6687 (mpp) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.3777 time to fit residues: 184.7637 Evaluate side-chains 209 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 322 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 641 GLN A 809 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN A1061 ASN C 440 GLN C1148 ASN B 31 ASN B 489 GLN B1028 GLN B1140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 29962 Z= 0.351 Angle : 0.736 10.691 40798 Z= 0.378 Chirality : 0.049 0.571 4790 Planarity : 0.005 0.056 5206 Dihedral : 7.953 106.244 5211 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % 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: -0.64 (0.13), residues: 3491 helix: 0.75 (0.18), residues: 819 sheet: -0.01 (0.18), residues: 748 loop : -1.13 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 192 HIS 0.014 0.002 HIS C 252 PHE 0.025 0.002 PHE B 542 TYR 0.039 0.002 TYR C 282 ARG 0.006 0.001 ARG B1076 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 3.471 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: A 26 ARG cc_start: 0.6336 (mtm180) cc_final: 0.6003 (mpt180) REVERT: A 129 ILE cc_start: 0.8071 (pt) cc_final: 0.7670 (pt) REVERT: A 194 MET cc_start: 0.7047 (mmm) cc_final: 0.6763 (tmm) REVERT: A 203 TYR cc_start: 0.7016 (t80) cc_final: 0.6692 (t80) REVERT: A 307 LYS cc_start: 0.7449 (mttt) cc_final: 0.7208 (mtmt) REVERT: A 315 PRO cc_start: 0.8112 (Cg_endo) cc_final: 0.7819 (Cg_exo) REVERT: A 361 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6586 (mt-10) REVERT: A 729 TYR cc_start: 0.8170 (t80) cc_final: 0.7833 (t80) REVERT: A 787 ASN cc_start: 0.4312 (OUTLIER) cc_final: 0.2850 (t0) REVERT: A 809 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7495 (p0) REVERT: A 810 MET cc_start: 0.7089 (mpp) cc_final: 0.6863 (mpp) REVERT: A 916 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 944 ARG cc_start: 0.8281 (mmt90) cc_final: 0.8077 (mmt90) REVERT: A 961 LEU cc_start: 0.7645 (tp) cc_final: 0.7312 (tp) REVERT: C 125 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7521 (pm20) REVERT: C 248 MET cc_start: 0.8488 (ppp) cc_final: 0.8280 (tmm) REVERT: C 307 LYS cc_start: 0.7424 (tttt) cc_final: 0.7151 (tttm) REVERT: C 352 LYS cc_start: 0.8365 (pttt) cc_final: 0.8114 (mptt) REVERT: C 397 MET cc_start: 0.6138 (ttm) cc_final: 0.5394 (ttm) REVERT: C 661 ASP cc_start: 0.6612 (t70) cc_final: 0.6233 (t70) REVERT: C 698 GLU cc_start: 0.8283 (pp20) cc_final: 0.7997 (pp20) REVERT: C 724 ASN cc_start: 0.6850 (m110) cc_final: 0.6481 (m-40) REVERT: C 735 ASN cc_start: 0.7633 (m110) cc_final: 0.7212 (m110) REVERT: C 866 LEU cc_start: 0.7326 (mt) cc_final: 0.6943 (tt) REVERT: C 994 ASN cc_start: 0.8444 (t0) cc_final: 0.8075 (m110) REVERT: B 88 ASP cc_start: 0.7846 (t0) cc_final: 0.7183 (t0) REVERT: B 121 VAL cc_start: 0.7214 (t) cc_final: 0.6850 (t) REVERT: B 163 LEU cc_start: 0.8167 (tt) cc_final: 0.7728 (tp) REVERT: B 170 TYR cc_start: 0.5427 (m-80) cc_final: 0.4564 (m-10) REVERT: B 209 TYR cc_start: 0.7693 (p90) cc_final: 0.6987 (p90) REVERT: B 217 TYR cc_start: 0.6379 (m-80) cc_final: 0.5904 (m-80) REVERT: B 725 TYR cc_start: 0.6840 (p90) cc_final: 0.6260 (p90) REVERT: B 882 LEU cc_start: 0.7611 (pp) cc_final: 0.7267 (mm) REVERT: B 892 ASP cc_start: 0.7571 (m-30) cc_final: 0.7323 (t0) REVERT: B 1005 THR cc_start: 0.7776 (m) cc_final: 0.7397 (p) REVERT: B 1053 ASN cc_start: 0.8688 (t0) cc_final: 0.8232 (m110) REVERT: B 1151 TYR cc_start: 0.6572 (m-80) cc_final: 0.6222 (m-80) REVERT: B 1197 MET cc_start: 0.8693 (mtp) cc_final: 0.8178 (mmm) REVERT: B 1229 TYR cc_start: 0.7912 (t80) cc_final: 0.7679 (t80) outliers start: 3 outliers final: 0 residues processed: 268 average time/residue: 0.4300 time to fit residues: 192.3739 Evaluate side-chains 187 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 359 optimal weight: 30.0000 chunk 298 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.0000 chunk 188 optimal weight: 10.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1147 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 GLN B1140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 29962 Z= 0.310 Angle : 0.700 9.404 40798 Z= 0.360 Chirality : 0.047 0.460 4790 Planarity : 0.005 0.053 5206 Dihedral : 7.979 104.050 5211 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % 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: -0.74 (0.14), residues: 3491 helix: 0.80 (0.18), residues: 812 sheet: -0.09 (0.18), residues: 744 loop : -1.24 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 192 HIS 0.008 0.002 HIS C 177 PHE 0.023 0.002 PHE B1020 TYR 0.048 0.002 TYR C 282 ARG 0.006 0.001 ARG B1076 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 2.762 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 26 ARG cc_start: 0.6436 (mtm180) cc_final: 0.6086 (mpt180) REVERT: A 194 MET cc_start: 0.7066 (mmm) cc_final: 0.6805 (tmm) REVERT: A 203 TYR cc_start: 0.6974 (t80) cc_final: 0.6624 (t80) REVERT: A 248 MET cc_start: 0.7381 (mpp) cc_final: 0.6999 (mpp) REVERT: A 307 LYS cc_start: 0.7443 (mttt) cc_final: 0.7186 (mtmt) REVERT: A 315 PRO cc_start: 0.8062 (Cg_endo) cc_final: 0.7739 (Cg_exo) REVERT: A 361 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6623 (mt-10) REVERT: A 729 TYR cc_start: 0.8145 (t80) cc_final: 0.7769 (t80) REVERT: A 809 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7430 (p0) REVERT: A 810 MET cc_start: 0.7190 (mpp) cc_final: 0.6951 (mpp) REVERT: A 916 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 961 LEU cc_start: 0.7646 (tp) cc_final: 0.7259 (tp) REVERT: A 1119 MET cc_start: 0.7751 (mtm) cc_final: 0.7430 (mtm) REVERT: A 1197 MET cc_start: 0.4801 (mmm) cc_final: 0.4476 (mmm) REVERT: C 125 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7505 (pm20) REVERT: C 248 MET cc_start: 0.8412 (ppp) cc_final: 0.8164 (tmm) REVERT: C 307 LYS cc_start: 0.7445 (tttt) cc_final: 0.7176 (tttm) REVERT: C 352 LYS cc_start: 0.8426 (pttt) cc_final: 0.8202 (mptt) REVERT: C 397 MET cc_start: 0.5892 (ttm) cc_final: 0.5105 (ttm) REVERT: C 661 ASP cc_start: 0.6497 (t70) cc_final: 0.6139 (t70) REVERT: C 698 GLU cc_start: 0.8202 (pp20) cc_final: 0.7908 (pp20) REVERT: C 724 ASN cc_start: 0.7067 (m110) cc_final: 0.6612 (m-40) REVERT: C 735 ASN cc_start: 0.7642 (m110) cc_final: 0.7254 (m110) REVERT: C 866 LEU cc_start: 0.7246 (mt) cc_final: 0.6853 (tt) REVERT: C 994 ASN cc_start: 0.8450 (t0) cc_final: 0.8050 (m110) REVERT: B 122 MET cc_start: 0.8080 (tpt) cc_final: 0.7753 (tpt) REVERT: B 187 HIS cc_start: 0.2190 (m-70) cc_final: 0.1647 (m-70) REVERT: B 217 TYR cc_start: 0.6279 (m-80) cc_final: 0.5688 (m-80) REVERT: B 725 TYR cc_start: 0.6865 (p90) cc_final: 0.6248 (p90) REVERT: B 892 ASP cc_start: 0.7529 (m-30) cc_final: 0.7242 (t0) REVERT: B 1005 THR cc_start: 0.7661 (m) cc_final: 0.7225 (p) REVERT: B 1053 ASN cc_start: 0.8711 (t0) cc_final: 0.8241 (m110) REVERT: B 1182 ILE cc_start: 0.7965 (tp) cc_final: 0.7757 (tp) REVERT: B 1197 MET cc_start: 0.8707 (mtp) cc_final: 0.8275 (mmm) REVERT: B 1229 TYR cc_start: 0.7970 (t80) cc_final: 0.7720 (t80) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.3635 time to fit residues: 149.0514 Evaluate side-chains 182 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 358 optimal weight: 40.0000 chunk 224 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 171 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 GLN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29962 Z= 0.211 Angle : 0.623 10.435 40798 Z= 0.322 Chirality : 0.046 0.490 4790 Planarity : 0.004 0.053 5206 Dihedral : 7.606 103.864 5211 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -0.58 (0.14), residues: 3491 helix: 1.08 (0.19), residues: 810 sheet: -0.08 (0.18), residues: 758 loop : -1.18 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 192 HIS 0.007 0.001 HIS C 177 PHE 0.021 0.002 PHE C 930 TYR 0.041 0.002 TYR B 282 ARG 0.005 0.000 ARG B1076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.409 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: A 26 ARG cc_start: 0.6472 (mtm180) cc_final: 0.6204 (mpt180) REVERT: A 129 ILE cc_start: 0.8082 (pt) cc_final: 0.7531 (pt) REVERT: A 194 MET cc_start: 0.7009 (mmm) cc_final: 0.6690 (tmm) REVERT: A 203 TYR cc_start: 0.6941 (t80) cc_final: 0.6655 (t80) REVERT: A 248 MET cc_start: 0.7370 (mpp) cc_final: 0.6997 (mpp) REVERT: A 307 LYS cc_start: 0.7439 (mttt) cc_final: 0.7179 (mtmt) REVERT: A 315 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: A 361 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6617 (mt-10) REVERT: A 416 ASP cc_start: 0.7920 (m-30) cc_final: 0.7438 (p0) REVERT: A 433 ASP cc_start: 0.8284 (t0) cc_final: 0.8036 (t70) REVERT: A 625 ILE cc_start: 0.8394 (mt) cc_final: 0.8045 (tp) REVERT: A 916 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7102 (mt-10) REVERT: A 961 LEU cc_start: 0.7741 (tp) cc_final: 0.7336 (tp) REVERT: A 1119 MET cc_start: 0.7688 (mtm) cc_final: 0.7346 (mtm) REVERT: A 1197 MET cc_start: 0.4780 (mmm) cc_final: 0.4428 (mmm) REVERT: C 125 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7410 (pm20) REVERT: C 248 MET cc_start: 0.8548 (ppp) cc_final: 0.8256 (tmm) REVERT: C 307 LYS cc_start: 0.7424 (tttt) cc_final: 0.7112 (tttm) REVERT: C 352 LYS cc_start: 0.8490 (pttt) cc_final: 0.8236 (mptt) REVERT: C 397 MET cc_start: 0.6069 (ttm) cc_final: 0.5300 (ttm) REVERT: C 538 ASP cc_start: 0.7181 (m-30) cc_final: 0.6324 (p0) REVERT: C 589 ASP cc_start: 0.8261 (t0) cc_final: 0.7677 (p0) REVERT: C 661 ASP cc_start: 0.6533 (t70) cc_final: 0.6213 (t70) REVERT: C 698 GLU cc_start: 0.8164 (pp20) cc_final: 0.7873 (pp20) REVERT: C 724 ASN cc_start: 0.7170 (m110) cc_final: 0.6786 (m110) REVERT: C 735 ASN cc_start: 0.7219 (m110) cc_final: 0.6913 (m110) REVERT: C 866 LEU cc_start: 0.7240 (mt) cc_final: 0.6875 (tt) REVERT: B 66 LEU cc_start: 0.6668 (mp) cc_final: 0.6456 (mp) REVERT: B 88 ASP cc_start: 0.7977 (t0) cc_final: 0.7418 (t0) REVERT: B 194 MET cc_start: 0.3381 (ttm) cc_final: 0.3108 (mtt) REVERT: B 217 TYR cc_start: 0.6364 (m-80) cc_final: 0.5751 (m-80) REVERT: B 416 ASP cc_start: 0.7768 (m-30) cc_final: 0.7558 (m-30) REVERT: B 470 SER cc_start: 0.7519 (m) cc_final: 0.7220 (t) REVERT: B 725 TYR cc_start: 0.6713 (p90) cc_final: 0.6146 (p90) REVERT: B 759 TYR cc_start: 0.7106 (t80) cc_final: 0.6845 (t80) REVERT: B 882 LEU cc_start: 0.7670 (pp) cc_final: 0.7263 (mm) REVERT: B 892 ASP cc_start: 0.7532 (m-30) cc_final: 0.7258 (t0) REVERT: B 1005 THR cc_start: 0.7659 (m) cc_final: 0.7281 (p) REVERT: B 1053 ASN cc_start: 0.8756 (t0) cc_final: 0.8297 (m110) REVERT: B 1108 SER cc_start: 0.9011 (t) cc_final: 0.8810 (p) REVERT: B 1182 ILE cc_start: 0.8020 (tp) cc_final: 0.7781 (tp) REVERT: B 1197 MET cc_start: 0.8701 (mtp) cc_final: 0.8272 (mmm) REVERT: B 1229 TYR cc_start: 0.7901 (t80) cc_final: 0.7615 (t80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3795 time to fit residues: 162.0437 Evaluate side-chains 192 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 69 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 281 optimal weight: 6.9990 overall best weight: 1.6152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 171 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29962 Z= 0.174 Angle : 0.592 8.695 40798 Z= 0.307 Chirality : 0.045 0.466 4790 Planarity : 0.004 0.056 5206 Dihedral : 7.301 110.740 5211 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 (0.14), residues: 3491 helix: 1.17 (0.19), residues: 817 sheet: -0.03 (0.18), residues: 761 loop : -1.05 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.005 0.001 HIS B 187 PHE 0.036 0.001 PHE A 399 TYR 0.048 0.002 TYR B 170 ARG 0.004 0.000 ARG A 944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.917 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 26 ARG cc_start: 0.6484 (mtm180) cc_final: 0.6249 (mpt180) REVERT: A 194 MET cc_start: 0.7000 (mmm) cc_final: 0.6710 (tmm) REVERT: A 203 TYR cc_start: 0.6913 (t80) cc_final: 0.6598 (t80) REVERT: A 248 MET cc_start: 0.7320 (mpp) cc_final: 0.6946 (mpp) REVERT: A 307 LYS cc_start: 0.7437 (mttt) cc_final: 0.7153 (mtmt) REVERT: A 315 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7855 (Cg_exo) REVERT: A 416 ASP cc_start: 0.7677 (m-30) cc_final: 0.7396 (p0) REVERT: A 625 ILE cc_start: 0.8301 (mt) cc_final: 0.8026 (tp) REVERT: A 679 MET cc_start: 0.7480 (mtt) cc_final: 0.7040 (mtm) REVERT: A 729 TYR cc_start: 0.8247 (t80) cc_final: 0.7890 (t80) REVERT: A 916 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 1119 MET cc_start: 0.7625 (mtm) cc_final: 0.7360 (mtm) REVERT: A 1197 MET cc_start: 0.4750 (mmm) cc_final: 0.4403 (mmm) REVERT: C 125 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7398 (pm20) REVERT: C 248 MET cc_start: 0.8610 (ppp) cc_final: 0.8332 (tmm) REVERT: C 307 LYS cc_start: 0.7393 (tttt) cc_final: 0.7111 (tttm) REVERT: C 352 LYS cc_start: 0.8510 (pttt) cc_final: 0.8259 (mptt) REVERT: C 397 MET cc_start: 0.6098 (ttm) cc_final: 0.5600 (ttm) REVERT: C 589 ASP cc_start: 0.8255 (t0) cc_final: 0.7682 (p0) REVERT: C 661 ASP cc_start: 0.6543 (t70) cc_final: 0.6221 (t70) REVERT: C 698 GLU cc_start: 0.8153 (pp20) cc_final: 0.7855 (pp20) REVERT: C 724 ASN cc_start: 0.7227 (m110) cc_final: 0.6750 (m110) REVERT: C 725 TYR cc_start: 0.7817 (p90) cc_final: 0.7338 (p90) REVERT: C 735 ASN cc_start: 0.7136 (m110) cc_final: 0.6873 (m110) REVERT: C 824 ASP cc_start: 0.8866 (t0) cc_final: 0.8617 (t0) REVERT: C 866 LEU cc_start: 0.7240 (mt) cc_final: 0.6882 (tt) REVERT: C 994 ASN cc_start: 0.8431 (t0) cc_final: 0.8069 (m110) REVERT: B 66 LEU cc_start: 0.6637 (mp) cc_final: 0.6414 (mp) REVERT: B 135 PHE cc_start: 0.7094 (m-80) cc_final: 0.6798 (m-10) REVERT: B 187 HIS cc_start: 0.2156 (m-70) cc_final: 0.1670 (m-70) REVERT: B 194 MET cc_start: 0.3600 (ttm) cc_final: 0.3179 (mtt) REVERT: B 217 TYR cc_start: 0.6219 (m-80) cc_final: 0.5615 (m-80) REVERT: B 470 SER cc_start: 0.7536 (m) cc_final: 0.7227 (t) REVERT: B 725 TYR cc_start: 0.6684 (p90) cc_final: 0.6117 (p90) REVERT: B 759 TYR cc_start: 0.7071 (t80) cc_final: 0.6773 (t80) REVERT: B 882 LEU cc_start: 0.7592 (pp) cc_final: 0.7172 (mm) REVERT: B 892 ASP cc_start: 0.7533 (m-30) cc_final: 0.7296 (t0) REVERT: B 1005 THR cc_start: 0.7645 (m) cc_final: 0.7300 (p) REVERT: B 1053 ASN cc_start: 0.8723 (t0) cc_final: 0.8293 (m110) REVERT: B 1108 SER cc_start: 0.9007 (t) cc_final: 0.8802 (p) REVERT: B 1197 MET cc_start: 0.8640 (mtp) cc_final: 0.8225 (mmm) REVERT: B 1229 TYR cc_start: 0.7901 (t80) cc_final: 0.7627 (t80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3596 time to fit residues: 160.2167 Evaluate side-chains 196 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 313 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 870 ASN B 429 ASN ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29962 Z= 0.205 Angle : 0.602 9.795 40798 Z= 0.310 Chirality : 0.045 0.477 4790 Planarity : 0.004 0.062 5206 Dihedral : 7.199 110.742 5211 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.47 (0.14), residues: 3491 helix: 1.13 (0.18), residues: 824 sheet: -0.03 (0.18), residues: 754 loop : -1.09 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 586 HIS 0.006 0.001 HIS B 187 PHE 0.026 0.002 PHE A 399 TYR 0.035 0.002 TYR C 282 ARG 0.006 0.000 ARG A 944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.687 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 26 ARG cc_start: 0.6515 (mtm180) cc_final: 0.6252 (mpt180) REVERT: A 194 MET cc_start: 0.7004 (mmm) cc_final: 0.6623 (tmm) REVERT: A 203 TYR cc_start: 0.6911 (t80) cc_final: 0.6616 (t80) REVERT: A 248 MET cc_start: 0.7374 (mpp) cc_final: 0.7002 (mpp) REVERT: A 307 LYS cc_start: 0.7403 (mttt) cc_final: 0.7112 (mtmt) REVERT: A 315 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: A 416 ASP cc_start: 0.7838 (m-30) cc_final: 0.7468 (p0) REVERT: A 433 ASP cc_start: 0.8247 (t0) cc_final: 0.7994 (t0) REVERT: A 625 ILE cc_start: 0.8310 (mt) cc_final: 0.8009 (tp) REVERT: A 679 MET cc_start: 0.7435 (mtt) cc_final: 0.7064 (mtm) REVERT: A 916 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 961 LEU cc_start: 0.7803 (tp) cc_final: 0.7451 (tp) REVERT: A 1119 MET cc_start: 0.7627 (mtm) cc_final: 0.7274 (mtm) REVERT: A 1197 MET cc_start: 0.4738 (mmm) cc_final: 0.4392 (mmm) REVERT: C 125 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7472 (pm20) REVERT: C 248 MET cc_start: 0.8613 (ppp) cc_final: 0.8329 (tmm) REVERT: C 307 LYS cc_start: 0.7402 (tttt) cc_final: 0.7116 (tttm) REVERT: C 352 LYS cc_start: 0.8511 (pttt) cc_final: 0.8256 (mptt) REVERT: C 397 MET cc_start: 0.6076 (ttm) cc_final: 0.5583 (ttm) REVERT: C 589 ASP cc_start: 0.8246 (t0) cc_final: 0.7689 (p0) REVERT: C 661 ASP cc_start: 0.6460 (t70) cc_final: 0.6168 (t70) REVERT: C 698 GLU cc_start: 0.8170 (pp20) cc_final: 0.7844 (pp20) REVERT: C 724 ASN cc_start: 0.7077 (m110) cc_final: 0.6655 (m110) REVERT: C 725 TYR cc_start: 0.7911 (p90) cc_final: 0.7459 (p90) REVERT: C 735 ASN cc_start: 0.7095 (m110) cc_final: 0.6810 (m110) REVERT: C 824 ASP cc_start: 0.8903 (t0) cc_final: 0.8674 (t0) REVERT: C 866 LEU cc_start: 0.7271 (mt) cc_final: 0.6908 (tt) REVERT: B 66 LEU cc_start: 0.6781 (mp) cc_final: 0.6380 (mp) REVERT: B 135 PHE cc_start: 0.6923 (m-80) cc_final: 0.6681 (m-80) REVERT: B 172 MET cc_start: 0.7197 (ptp) cc_final: 0.6906 (ptp) REVERT: B 187 HIS cc_start: 0.2088 (m-70) cc_final: 0.1604 (m-70) REVERT: B 191 LEU cc_start: 0.7436 (tp) cc_final: 0.6769 (tp) REVERT: B 217 TYR cc_start: 0.6182 (m-80) cc_final: 0.5797 (m-80) REVERT: B 725 TYR cc_start: 0.6764 (p90) cc_final: 0.6190 (p90) REVERT: B 759 TYR cc_start: 0.7068 (t80) cc_final: 0.6785 (t80) REVERT: B 882 LEU cc_start: 0.7612 (pp) cc_final: 0.7167 (mm) REVERT: B 892 ASP cc_start: 0.7571 (m-30) cc_final: 0.7345 (t0) REVERT: B 1005 THR cc_start: 0.7657 (m) cc_final: 0.7329 (p) REVERT: B 1053 ASN cc_start: 0.8704 (t0) cc_final: 0.8307 (m110) REVERT: B 1197 MET cc_start: 0.8699 (mtp) cc_final: 0.8315 (mmm) REVERT: B 1229 TYR cc_start: 0.7974 (t80) cc_final: 0.7724 (t80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3511 time to fit residues: 148.2634 Evaluate side-chains 199 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.5980 chunk 353 optimal weight: 50.0000 chunk 215 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 171 ASN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29962 Z= 0.283 Angle : 0.667 10.393 40798 Z= 0.345 Chirality : 0.046 0.475 4790 Planarity : 0.005 0.062 5206 Dihedral : 7.609 117.069 5211 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.71 (0.14), residues: 3491 helix: 0.85 (0.18), residues: 821 sheet: -0.15 (0.18), residues: 773 loop : -1.22 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 192 HIS 0.006 0.001 HIS B 187 PHE 0.033 0.002 PHE A 399 TYR 0.039 0.002 TYR C 282 ARG 0.007 0.001 ARG A 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6982 Ramachandran restraints generated. 3491 Oldfield, 0 Emsley, 3491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6510 (mtm180) cc_final: 0.6066 (mpt180) REVERT: A 194 MET cc_start: 0.7016 (mmm) cc_final: 0.6629 (tmm) REVERT: A 203 TYR cc_start: 0.6946 (t80) cc_final: 0.6622 (t80) REVERT: A 248 MET cc_start: 0.7534 (mpp) cc_final: 0.6864 (mpp) REVERT: A 299 MET cc_start: 0.8247 (mmt) cc_final: 0.8026 (mmm) REVERT: A 307 LYS cc_start: 0.7451 (mttt) cc_final: 0.7193 (mtmt) REVERT: A 315 PRO cc_start: 0.8098 (Cg_endo) cc_final: 0.7812 (Cg_exo) REVERT: A 433 ASP cc_start: 0.8137 (t0) cc_final: 0.7922 (t70) REVERT: A 625 ILE cc_start: 0.8338 (mt) cc_final: 0.7983 (tp) REVERT: A 679 MET cc_start: 0.7397 (mtt) cc_final: 0.7048 (mtm) REVERT: A 810 MET cc_start: 0.7119 (mpp) cc_final: 0.6903 (mpp) REVERT: A 916 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 961 LEU cc_start: 0.7750 (tp) cc_final: 0.7348 (tp) REVERT: A 1119 MET cc_start: 0.7616 (mtm) cc_final: 0.7275 (mtm) REVERT: A 1197 MET cc_start: 0.4871 (mmm) cc_final: 0.4569 (mmm) REVERT: C 125 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7527 (pm20) REVERT: C 248 MET cc_start: 0.8686 (ppp) cc_final: 0.8377 (tmm) REVERT: C 307 LYS cc_start: 0.7486 (tttt) cc_final: 0.7207 (tttm) REVERT: C 352 LYS cc_start: 0.8489 (pttt) cc_final: 0.8225 (mptt) REVERT: C 397 MET cc_start: 0.6061 (ttm) cc_final: 0.5292 (ttm) REVERT: C 589 ASP cc_start: 0.8244 (t0) cc_final: 0.7699 (p0) REVERT: C 661 ASP cc_start: 0.7072 (t70) cc_final: 0.6716 (t70) REVERT: C 698 GLU cc_start: 0.8256 (pp20) cc_final: 0.7899 (pp20) REVERT: C 725 TYR cc_start: 0.7850 (p90) cc_final: 0.7303 (p90) REVERT: C 735 ASN cc_start: 0.7438 (m110) cc_final: 0.7077 (m110) REVERT: C 824 ASP cc_start: 0.8859 (t0) cc_final: 0.8624 (t0) REVERT: B 88 ASP cc_start: 0.7766 (t70) cc_final: 0.7483 (t0) REVERT: B 135 PHE cc_start: 0.6852 (m-80) cc_final: 0.6609 (m-80) REVERT: B 172 MET cc_start: 0.6942 (ptp) cc_final: 0.6589 (ptp) REVERT: B 217 TYR cc_start: 0.6192 (m-80) cc_final: 0.5807 (m-80) REVERT: B 725 TYR cc_start: 0.6722 (p90) cc_final: 0.6144 (p90) REVERT: B 759 TYR cc_start: 0.7257 (t80) cc_final: 0.6913 (t80) REVERT: B 1005 THR cc_start: 0.7687 (m) cc_final: 0.7341 (p) REVERT: B 1053 ASN cc_start: 0.8728 (t0) cc_final: 0.8319 (m110) REVERT: B 1197 MET cc_start: 0.8671 (mtp) cc_final: 0.8258 (mmm) REVERT: B 1229 TYR cc_start: 0.7960 (t80) cc_final: 0.7750 (t80) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3667 time to fit residues: 145.6585 Evaluate side-chains 184 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** B 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.050410 restraints weight = 143206.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051650 restraints weight = 87154.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052257 restraints weight = 57836.584| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 29962 Z= 0.354 Angle : 0.738 11.297 40798 Z= 0.378 Chirality : 0.048 0.488 4790 Planarity : 0.005 0.064 5206 Dihedral : 8.169 129.677 5211 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.01 (0.14), residues: 3491 helix: 0.61 (0.18), residues: 795 sheet: -0.27 (0.19), residues: 747 loop : -1.41 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 586 HIS 0.007 0.002 HIS B1157 PHE 0.031 0.002 PHE A 399 TYR 0.040 0.002 TYR C 282 ARG 0.007 0.001 ARG A 944 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5359.38 seconds wall clock time: 99 minutes 0.01 seconds (5940.01 seconds total)