Starting phenix.real_space_refine on Mon Nov 20 08:36:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb5_24970/11_2023/7sb5_24970_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 18696 2.51 5 N 4799 2.21 5 O 5773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 361": "OE1" <-> "OE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 29457 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 9183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9183 Classifications: {'peptide': 1180} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "B" Number of atoms: 9202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9202 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 51, 'TRANS': 1131} Chain breaks: 5 Chain: "A" Number of atoms: 9229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9229 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 52, 'TRANS': 1134} Chain breaks: 5 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 176 Unusual residues: {'NAG': 10, 'PLM': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PLM': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.16, per 1000 atoms: 0.51 Number of scatterers: 29457 At special positions: 0 Unit cell: (181.28, 169.95, 159.65, 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 5773 8.00 N 4799 7.00 C 18696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 173 " distance=2.03 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=2.09 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.02 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.05 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 825 " - pdb=" SG CYS C 847 " distance=2.06 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=2.07 Simple disulfide: pdb=" SG CYS C1125 " - pdb=" SG CYS C1136 " distance=2.02 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.10 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.04 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=2.07 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.05 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.02 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=2.04 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.05 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.03 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=2.06 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.04 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.04 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 212 " " NAG A1402 " - " ASN A 449 " " 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 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 B 675 " " NAG B1407 " - " ASN B 695 " " NAG B1408 " - " ASN B 648 " " NAG B1409 " - " ASN B 371 " " NAG B1410 " - " ASN B1223 " " NAG C1401 " - " ASN C 137 " " NAG C1402 " - " ASN C 212 " " NAG C1403 " - " ASN C 713 " " NAG C1404 " - " ASN C 936 " " NAG C1405 " - " ASN C1193 " " NAG C1406 " - " ASN C 675 " " NAG C1407 " - " ASN C 695 " " NAG C1408 " - " ASN C 648 " " NAG C1409 " - " ASN C 449 " " NAG C1410 " - " ASN C1223 " " NAG C1411 " - " ASN C 787 " " NAG D 1 " - " ASN C 738 " " NAG E 1 " - " ASN C 206 " " NAG F 1 " - " ASN C 371 " " NAG G 1 " - " ASN B 137 " " NAG I 1 " - " ASN B 738 " " NAG J 1 " - " ASN B1193 " " NAG K 1 " - " ASN B 206 " " NAG M 1 " - " ASN A 137 " " NAG N 1 " - " ASN A 371 " " NAG O 1 " - " ASN A 738 " " NAG P 1 " - " ASN A 206 " Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 5.2 seconds 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 49 sheets defined 22.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 372 through 378 removed outlier: 4.687A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) 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 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 425 through 428 No H-bonds generated for 'chain 'C' and resid 425 through 428' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' 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 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' 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 829 Processing helix chain 'C' and resid 834 through 873 removed outlier: 4.651A pdb=" N GLU C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) removed outlier: 4.175A 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: 7.046A pdb=" N PHE C 846 " --> pdb=" O GLU C 842 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS C 847 " --> pdb=" O TYR C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 883 No H-bonds generated for 'chain 'C' and resid 881 through 883' Processing helix chain 'C' and resid 914 through 920 Processing helix chain 'C' and resid 927 through 934 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 1001 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: 3.654A pdb=" N LEU C1059 " --> pdb=" O LEU C1055 " (cutoff:3.500A) removed outlier: 4.290A 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 1124 removed outlier: 3.959A 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 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 373 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 Processing helix chain 'B' and resid 425 through 428 No H-bonds generated for 'chain 'B' and resid 425 through 428' 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 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' 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: 4.400A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 883 removed outlier: 3.575A pdb=" N LYS B 883 " --> pdb=" O THR B 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 880 through 883' Processing helix chain 'B' and resid 914 through 922 removed outlier: 4.052A pdb=" N LYS B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 946 through 953 Processing helix chain 'B' and resid 964 through 978 removed outlier: 4.053A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) 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 1060 removed outlier: 4.068A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1125 removed outlier: 4.933A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B1085 " --> pdb=" O GLU B1081 " (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 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 345 through 349 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 423 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: 3.622A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 883 Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 938 No H-bonds generated for 'chain 'A' and resid 936 through 938' Processing helix chain 'A' and resid 946 through 953 Processing helix chain 'A' and resid 964 through 979 Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.713A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1029 Processing helix chain 'A' and resid 1036 through 1059 removed outlier: 3.500A pdb=" N VAL A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 4.132A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id= A, first strand: chain 'C' and resid 64 through 73 removed outlier: 3.576A pdb=" N ASN C 294 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 272 through 276 removed outlier: 5.447A pdb=" N PHE C 231 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE C 240 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 114 through 118 Processing sheet with id= D, first strand: chain 'C' and resid 252 through 255 Processing sheet with id= E, first strand: chain 'C' and resid 318 through 321 Processing sheet with id= F, first strand: chain 'C' and resid 331 through 335 removed outlier: 3.560A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 667 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 659 " --> pdb=" O TYR C 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.137A pdb=" N SER C 451 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.629A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 383 " --> pdb=" O TYR C 442 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 485 through 488 Processing sheet with id= J, first strand: chain 'C' and resid 491 through 493 removed outlier: 4.354A pdb=" N CYS C 491 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 701 through 704 Processing sheet with id= L, first strand: chain 'C' and resid 755 through 759 Processing sheet with id= M, first strand: chain 'C' and resid 797 through 802 Processing sheet with id= N, first strand: chain 'C' and resid 805 through 815 removed outlier: 3.578A pdb=" N ILE C1143 " --> pdb=" O PHE C1158 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR C1160 " --> pdb=" O HIS C1141 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS C1141 " --> pdb=" O TYR C1160 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 820 through 823 removed outlier: 4.005A pdb=" N LYS C 820 " --> pdb=" O LEU C 958 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1174 through 1176 removed outlier: 3.724A pdb=" N ARG C1180 " --> pdb=" O ILE C1176 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1187 through 1192 Processing sheet with id= R, first strand: chain 'B' and resid 64 through 73 Processing sheet with id= S, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.388A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= U, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= V, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= W, first strand: chain 'B' and resid 324 through 326 Processing sheet with id= X, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.042A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.520A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AA, first strand: chain 'B' and resid 630 through 635 removed outlier: 4.353A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 773 through 777 removed outlier: 6.468A pdb=" N VAL B 757 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR B 750 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 796 through 802 Processing sheet with id= AD, first strand: chain 'B' and resid 805 through 815 removed outlier: 3.508A pdb=" N ILE B1143 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR B1160 " --> pdb=" O HIS B1141 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B1141 " --> pdb=" O TYR B1160 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 820 through 823 removed outlier: 3.978A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= AG, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id= AH, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= AI, first strand: chain 'A' and resid 64 through 73 Processing sheet with id= AJ, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.505A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= AL, first strand: chain 'A' and resid 252 through 255 Processing sheet with id= AM, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= AN, first strand: chain 'A' and resid 331 through 335 removed outlier: 3.629A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.046A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.162A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.604A pdb=" N SER A 587 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'A' and resid 755 through 759 Processing sheet with id= AS, first strand: chain 'A' and resid 805 through 815 removed outlier: 5.930A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.295A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 1225 through 1227 Processing sheet with id= AV, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AW, first strand: chain 'A' and resid 797 through 804 removed outlier: 6.462A pdb=" N LYS A1164 " --> pdb=" O SER A 803 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2727 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: 11.79 Time building geometry restraints manager: 12.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 7999 1.33 - 1.47: 9749 1.47 - 1.62: 12087 1.62 - 1.76: 32 1.76 - 1.91: 223 Bond restraints: 30090 Sorted by residual: bond pdb=" C6 PLM B1411 " pdb=" C7 PLM B1411 " ideal model delta sigma weight residual 1.525 1.360 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C6 PLM B1412 " pdb=" C7 PLM B1412 " ideal model delta sigma weight residual 1.525 1.361 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C6 PLM A1411 " pdb=" C7 PLM A1411 " ideal model delta sigma weight residual 1.525 1.361 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" CB HIS B 483 " pdb=" CG HIS B 483 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.51e+01 bond pdb=" CB HIS B1141 " pdb=" CG HIS B1141 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.32e+01 ... (remaining 30085 not shown) Histogram of bond angle deviations from ideal: 96.30 - 103.89: 423 103.89 - 111.49: 12428 111.49 - 119.09: 12090 119.09 - 126.69: 15795 126.69 - 134.28: 242 Bond angle restraints: 40978 Sorted by residual: angle pdb=" C ALA C 314 " pdb=" N PRO C 315 " pdb=" CA PRO C 315 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.30e-01 1.88e+00 8.81e+01 angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.21 129.05 -8.84 9.60e-01 1.09e+00 8.49e+01 angle pdb=" C PRO C 959 " pdb=" N PRO C 960 " pdb=" CA PRO C 960 " ideal model delta sigma weight residual 120.03 128.83 -8.80 9.90e-01 1.02e+00 7.89e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.21 128.37 -8.16 9.60e-01 1.09e+00 7.23e+01 angle pdb=" C GLY C 544 " pdb=" N PRO C 545 " pdb=" CA PRO C 545 " ideal model delta sigma weight residual 120.04 128.79 -8.75 1.08e+00 8.57e-01 6.56e+01 ... (remaining 40973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 16820 17.47 - 34.93: 487 34.93 - 52.40: 117 52.40 - 69.86: 55 69.86 - 87.33: 18 Dihedral angle restraints: 17497 sinusoidal: 6515 harmonic: 10982 Sorted by residual: dihedral pdb=" CB CYS A 830 " pdb=" SG CYS A 830 " pdb=" SG CYS A 836 " pdb=" CB CYS A 836 " ideal model delta sinusoidal sigma weight residual 93.00 164.23 -71.23 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" N SER C 739 " pdb=" C SER C 739 " pdb=" CA SER C 739 " pdb=" CB SER C 739 " ideal model delta harmonic sigma weight residual 122.80 102.76 20.04 0 2.50e+00 1.60e-01 6.43e+01 dihedral pdb=" CB CYS B 747 " pdb=" SG CYS B 747 " pdb=" SG CYS B 756 " pdb=" CB CYS B 756 " ideal model delta sinusoidal sigma weight residual 93.00 27.74 65.26 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 17494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3819 0.126 - 0.252: 809 0.252 - 0.377: 128 0.377 - 0.503: 56 0.503 - 0.629: 3 Chirality restraints: 4815 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.64e+02 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 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 ... (remaining 4812 not shown) Planarity restraints: 5270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1404 " 0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG B1404 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1404 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG B1404 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1404 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " 0.186 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG A1404 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " -0.252 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.145 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG F 2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.196 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.116 2.00e-02 2.50e+03 ... (remaining 5267 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1604 2.69 - 3.24: 29356 3.24 - 3.80: 49094 3.80 - 4.35: 63935 4.35 - 4.90: 101407 Nonbonded interactions: 245396 Sorted by model distance: nonbonded pdb=" O3 NAG C1403 " pdb=" O7 NAG C1403 " model vdw 2.138 2.440 nonbonded pdb=" O3 NAG C1409 " pdb=" O7 NAG C1409 " model vdw 2.158 2.440 nonbonded pdb=" O3 NAG B1402 " pdb=" O7 NAG B1402 " model vdw 2.182 2.440 nonbonded pdb=" O3 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.187 2.440 nonbonded pdb=" O3 NAG G 2 " pdb=" O7 NAG G 2 " model vdw 2.204 2.440 ... (remaining 245391 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 150 or resid 158 through 473 or resid 480 throu \ gh 762 or resid 772 through 1233 or resid 1401 through 1410)) selection = (chain 'B' and (resid 15 through 504 or resid 517 through 762 or resid 772 throu \ gh 1233 or resid 1401 through 1410)) selection = (chain 'C' and (resid 15 through 473 or resid 480 through 1233 or resid 1401 thr \ ough 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 13 through 109) 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.950 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 77.590 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.270 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.190 30090 Z= 1.338 Angle : 1.772 14.503 40978 Z= 1.182 Chirality : 0.113 0.629 4815 Planarity : 0.010 0.297 5228 Dihedral : 9.999 87.326 10268 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.23 % 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: 0.57 (0.13), residues: 3514 helix: 0.32 (0.16), residues: 819 sheet: 1.25 (0.17), residues: 731 loop : 0.18 (0.13), residues: 1964 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4169 time to fit residues: 70.8075 Evaluate side-chains 66 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 3.308 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 GLN C 663 ASN ** C 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1138 ASN B 342 ASN B 950 GLN B 996 GLN B1028 GLN B1138 ASN B1141 HIS A 219 HIS A 387 ASN A 440 GLN A 461 ASN A 490 HIS A 560 HIS A 609 ASN A 714 ASN A 994 ASN A 996 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30090 Z= 0.290 Angle : 0.674 10.099 40978 Z= 0.352 Chirality : 0.045 0.511 4815 Planarity : 0.004 0.041 5228 Dihedral : 6.242 59.505 4077 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.03 % Allowed : 1.00 % 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: 0.82 (0.14), residues: 3514 helix: 1.76 (0.18), residues: 817 sheet: 0.78 (0.18), residues: 731 loop : -0.01 (0.14), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.3788 time to fit residues: 52.4028 Evaluate side-chains 64 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 3.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 366 optimal weight: 30.0000 chunk 302 optimal weight: 8.9990 chunk 336 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 641 GLN C 663 ASN C 705 ASN C 996 GLN C1138 ASN B 219 HIS B 950 GLN A 935 ASN A1071 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 30090 Z= 0.314 Angle : 0.631 9.927 40978 Z= 0.331 Chirality : 0.044 0.295 4815 Planarity : 0.004 0.068 5228 Dihedral : 5.874 58.298 4077 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3514 helix: 1.83 (0.18), residues: 826 sheet: 0.50 (0.18), residues: 746 loop : -0.20 (0.14), residues: 1942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4351 time to fit residues: 53.6596 Evaluate side-chains 60 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 4.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 360 optimal weight: 50.0000 chunk 177 optimal weight: 9.9990 chunk 322 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN C 641 GLN ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A1157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 30090 Z= 0.339 Angle : 0.644 11.590 40978 Z= 0.329 Chirality : 0.043 0.331 4815 Planarity : 0.004 0.040 5228 Dihedral : 5.822 58.080 4077 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % 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: 0.32 (0.14), residues: 3514 helix: 1.65 (0.18), residues: 828 sheet: 0.31 (0.18), residues: 757 loop : -0.43 (0.14), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.3973 time to fit residues: 50.0586 Evaluate side-chains 62 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 3.576 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3093 time to fit residues: 5.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 8.9990 chunk 204 optimal weight: 0.0170 chunk 5 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 148 optimal weight: 0.0270 chunk 307 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN B 187 HIS B 369 ASN A 602 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30090 Z= 0.167 Angle : 0.519 8.903 40978 Z= 0.270 Chirality : 0.042 0.264 4815 Planarity : 0.003 0.040 5228 Dihedral : 5.498 59.273 4077 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: 0.53 (0.14), residues: 3514 helix: 1.94 (0.18), residues: 826 sheet: 0.52 (0.19), residues: 731 loop : -0.38 (0.14), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4109 time to fit residues: 53.9423 Evaluate side-chains 62 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 360 optimal weight: 50.0000 chunk 299 optimal weight: 0.0770 chunk 167 optimal weight: 40.0000 chunk 30 optimal weight: 0.0170 chunk 119 optimal weight: 0.2980 chunk 189 optimal weight: 5.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 602 ASN A 714 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30090 Z= 0.125 Angle : 0.493 9.908 40978 Z= 0.256 Chirality : 0.041 0.222 4815 Planarity : 0.003 0.043 5228 Dihedral : 5.145 59.933 4077 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.65 (0.14), residues: 3514 helix: 2.10 (0.19), residues: 826 sheet: 0.61 (0.19), residues: 731 loop : -0.35 (0.14), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3902 time to fit residues: 55.3361 Evaluate side-chains 64 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 303 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 359 optimal weight: 50.0000 chunk 224 optimal weight: 1.9990 chunk 219 optimal weight: 0.0970 chunk 165 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30090 Z= 0.142 Angle : 0.488 8.587 40978 Z= 0.253 Chirality : 0.041 0.217 4815 Planarity : 0.003 0.046 5228 Dihedral : 4.898 56.474 4077 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.66 (0.14), residues: 3514 helix: 2.15 (0.19), residues: 827 sheet: 0.54 (0.19), residues: 739 loop : -0.33 (0.14), residues: 1948 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4025 time to fit residues: 54.4941 Evaluate side-chains 62 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 282 optimal weight: 9.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 30090 Z= 0.266 Angle : 0.557 8.991 40978 Z= 0.285 Chirality : 0.042 0.241 4815 Planarity : 0.004 0.045 5228 Dihedral : 5.002 52.814 4077 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.52 (0.14), residues: 3514 helix: 2.07 (0.19), residues: 826 sheet: 0.38 (0.18), residues: 763 loop : -0.41 (0.14), residues: 1925 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3974 time to fit residues: 47.7395 Evaluate side-chains 61 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 3.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 20.0000 chunk 344 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 335 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 302 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS A 602 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30090 Z= 0.239 Angle : 0.538 8.808 40978 Z= 0.277 Chirality : 0.041 0.238 4815 Planarity : 0.003 0.043 5228 Dihedral : 4.991 50.469 4077 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.41 (0.14), residues: 3514 helix: 1.99 (0.18), residues: 820 sheet: 0.34 (0.19), residues: 743 loop : -0.48 (0.14), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3926 time to fit residues: 47.7379 Evaluate side-chains 62 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.8980 chunk 354 optimal weight: 40.0000 chunk 216 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 371 optimal weight: 50.0000 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN A 609 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30090 Z= 0.149 Angle : 0.493 8.677 40978 Z= 0.255 Chirality : 0.041 0.221 4815 Planarity : 0.003 0.047 5228 Dihedral : 4.848 50.593 4077 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 0.49 (0.14), residues: 3514 helix: 2.04 (0.19), residues: 827 sheet: 0.43 (0.19), residues: 741 loop : -0.46 (0.14), residues: 1946 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3966 time to fit residues: 50.7242 Evaluate side-chains 62 residues out of total 3090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.8980 chunk 315 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.028308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.023322 restraints weight = 313403.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.023993 restraints weight = 170042.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.024450 restraints weight = 109592.004| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30090 Z= 0.158 Angle : 0.496 13.917 40978 Z= 0.254 Chirality : 0.041 0.219 4815 Planarity : 0.003 0.046 5228 Dihedral : 4.748 58.804 4077 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 3514 helix: 2.03 (0.18), residues: 833 sheet: 0.43 (0.19), residues: 717 loop : -0.48 (0.14), residues: 1964 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3778.30 seconds wall clock time: 72 minutes 51.05 seconds (4371.05 seconds total)