Starting phenix.real_space_refine on Sat Dec 9 22:03:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpg_37716/12_2023/8wpg_37716_updated.pdb" } resolution = 2.7 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= -0.002 sd= 0.085 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 62 5.16 5 C 8023 2.51 5 N 2030 2.21 5 O 2316 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6096 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6069 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "C" 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: "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: 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: "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: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CA': 3, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.45, per 1000 atoms: 0.52 Number of scatterers: 12443 At special positions: 0 Unit cell: (97.37, 89.88, 185.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 62 16.00 P 2 15.00 F 6 9.00 O 2316 8.00 N 2030 7.00 C 8023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.21 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 468 " " NAG C 1 " - " ASN B 541 " " NAG D 1 " - " ASN B 488 " " NAG E 1 " - " ASN A 488 " " NAG F 1 " - " ASN A 541 " Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.6 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 13 sheets defined 42.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.631A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 297 through 300 No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.453A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 613 through 636 Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.629A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 666 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.771A pdb=" N VAL B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 745 removed outlier: 3.796A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 790 Processing helix chain 'B' and resid 803 through 819 Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 835 through 852 removed outlier: 4.502A pdb=" N LEU B 842 " --> pdb=" O VAL B 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 857 No H-bonds generated for 'chain 'B' and resid 854 through 857' Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.660A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.650A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 667 removed outlier: 3.898A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 698 Processing helix chain 'A' and resid 725 through 745 removed outlier: 3.714A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 796 removed outlier: 3.714A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 790 " --> pdb=" O ILE A 786 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 819 removed outlier: 3.763A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.823A pdb=" N SER A 827 " --> pdb=" O PRO A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 860 removed outlier: 3.915A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.169A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.163A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.322A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= F, first strand: chain 'B' and resid 602 through 604 Processing sheet with id= G, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.320A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.515A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS A 236 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR A 211 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP A 238 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 12.525A pdb=" N ALA A 213 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N SER A 240 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.086A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= L, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.512A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3950 1.34 - 1.46: 3169 1.46 - 1.58: 5547 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 12740 Sorted by residual: bond pdb=" O4 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.568 1.503 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O2 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" O3 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" O2 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" O3 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 12735 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.97: 338 106.97 - 113.75: 7046 113.75 - 120.53: 4940 120.53 - 127.31: 4881 127.31 - 134.09: 141 Bond angle restraints: 17346 Sorted by residual: angle pdb=" N ILE A 819 " pdb=" CA ILE A 819 " pdb=" C ILE A 819 " ideal model delta sigma weight residual 112.96 108.16 4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N ASN B 867 " pdb=" CA ASN B 867 " pdb=" C ASN B 867 " ideal model delta sigma weight residual 108.07 114.46 -6.39 1.38e+00 5.25e-01 2.14e+01 angle pdb=" CA PRO A 682 " pdb=" N PRO A 682 " pdb=" CD PRO A 682 " ideal model delta sigma weight residual 112.00 106.51 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA LEU A 783 " pdb=" CB LEU A 783 " pdb=" CG LEU A 783 " ideal model delta sigma weight residual 116.30 129.24 -12.94 3.50e+00 8.16e-02 1.37e+01 angle pdb=" C PRO B 864 " pdb=" N SER B 865 " pdb=" CA SER B 865 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 17341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6598 17.66 - 35.32: 761 35.32 - 52.98: 224 52.98 - 70.64: 44 70.64 - 88.30: 16 Dihedral angle restraints: 7643 sinusoidal: 2967 harmonic: 4676 Sorted by residual: dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 179.02 -86.02 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual -86.00 -139.09 53.09 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 7640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1616 0.054 - 0.109: 315 0.109 - 0.163: 57 0.163 - 0.217: 1 0.217 - 0.272: 2 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILE B 816 " pdb=" CA ILE B 816 " pdb=" CG1 ILE B 816 " pdb=" CG2 ILE B 816 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA YP4 A 906 " pdb=" N YP4 A 906 " pdb=" CB YP4 A 906 " pdb=" C1 YP4 A 906 " both_signs ideal model delta sigma weight residual False -2.41 -2.64 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA YP4 B 909 " pdb=" N YP4 B 909 " pdb=" CB YP4 B 909 " pdb=" C1 YP4 B 909 " both_signs ideal model delta sigma weight residual False -2.41 -2.61 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1988 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 135 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 136 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 681 " -0.051 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 682 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 671 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 672 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " -0.031 5.00e-02 4.00e+02 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 432 2.71 - 3.26: 12422 3.26 - 3.81: 21137 3.81 - 4.35: 26390 4.35 - 4.90: 43515 Nonbonded interactions: 103896 Sorted by model distance: nonbonded pdb=" O TRP A 818 " pdb=" F1 YP4 A 906 " model vdw 2.163 2.390 nonbonded pdb=" O TRP B 818 " pdb=" F1 YP4 B 909 " model vdw 2.170 2.390 nonbonded pdb=" O ALA B 548 " pdb=" OG SER B 574 " model vdw 2.184 2.440 nonbonded pdb=" NH1 ARG B 69 " pdb=" O PRO B 407 " model vdw 2.187 2.520 nonbonded pdb=" O VAL B 314 " pdb=" OG1 THR B 317 " model vdw 2.189 2.440 ... (remaining 103891 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 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 359 or (resid 360 and (name N or n \ ame CA or name C or name O or name CB )) or resid 361 through 397 or (resid 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 44 \ 0 or (resid 441 and (name N or name CA or name C or name O or name CB )) or resi \ d 442 through 499 or (resid 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 515 or (resid 516 and (name N or name CA or name C \ or name O or name CB )) or resid 517 through 591 or (resid 592 through 593 and \ (name N or name CA or name C or name O or name CB )) or resid 594 through 603 or \ (resid 604 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 5 through 613 or (resid 614 through 615 and (name N or name CA or name C or name \ O or name CB )) or resid 616 through 630 or (resid 631 and (name N or name CA o \ r name C or name O or name CB )) or resid 632 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throug \ h 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or \ resid 640 through 643 or (resid 644 through 646 and (name N or name CA or name C \ or name O or name CB )) or resid 647 through 660 or (resid 661 and (name N or n \ ame CA or name C or name O or name CB )) or resid 662 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 or (resid \ 676 and (name N or name CA or name C or name O or name CB )) or resid 677 throug \ h 679 or (resid 680 through 681 and (name N or name CA or name C or name O or na \ me CB )) or resid 682 through 702 or resid 722 through 725 or (resid 726 and (na \ me N or name CA or name C or name O or name CB )) or resid 727 through 739 or (r \ esid 740 through 741 and (name N or name CA or name C or name O or name CB )) or \ resid 742 through 744 or (resid 745 through 746 and (name N or name CA or name \ C or name O or name CB )) or resid 747 through 785 or (resid 786 through 789 and \ (name N or name CA or name C or name O or name CB )) or resid 790 through 800 o \ r (resid 801 through 806 and (name N or name CA or name C or name O or name CB ) \ ) or resid 807 through 812 or (resid 813 and (name N or name CA or name C or nam \ e O or name CB )) or resid 814 through 826 or (resid 827 and (name N or name CA \ or name C or name O or name CB )) or resid 828 through 837 or (resid 838 and (na \ me N or name CA or name C or name O or name CB )) or resid 839 through 850 or (r \ esid 851 and (name N or name CA or name C or name O or name CB )) or resid 852 t \ hrough 854 or (resid 855 and (name N or name CA or name C or name O or name CB ) \ ) or resid 856 or (resid 857 and (name N or name CA or name C or name O or name \ CB )) or resid 858 through 860 or (resid 861 through 863 and (name N or name CA \ or name C or name O or name CB )) or resid 864 through 872 or resid 901 through \ 903 or resid 904)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB )) or resid 51 through 127 or (resid 131 through 135 an \ d (name N or name CA or name C or name O or name CB )) or resid 136 through 222 \ or (resid 223 and (name N or name CA or name C or name O or name CB )) or resid \ 224 through 261 or (resid 262 and (name N or name CA or name C or name O or name \ CB )) or resid 263 through 362 or resid 392 through 451 or (resid 452 through 4 \ 53 and (name N or name CA or name C or name O or name CB )) or resid 454 through \ 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) or r \ esid 514 through 525 or (resid 526 and (name N or name CA or name C or name O or \ name CB )) or resid 527 through 577 or (resid 578 through 579 and (name N or na \ me CA or name C or name O or name CB )) or resid 580 through 582 or (resid 583 t \ hrough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 586 or (resid 587 through 588 and (name N or name CA or name C or name \ O or name CB )) or resid 589 through 609 or (resid 610 and (name N or name CA or \ name C or name O or name CB )) or resid 611 through 620 or (resid 621 and (name \ N or name CA or name C or name O or name CB )) or resid 622 through 623 or (res \ id 624 through 625 and (name N or name CA or name C or name O or name CB )) or r \ esid 626 through 648 or (resid 649 and (name N or name CA or name C or name O or \ name CB )) or resid 650 through 652 or (resid 653 and (name N or name CA or nam \ e C or name O or name CB )) or resid 654 through 658 or (resid 659 and (name N o \ r name CA or name C or name O or name CB )) or resid 660 through 664 or (resid 6 \ 65 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 668 or (resid 669 and (name N or name CA or name C or name O or name CB )) or r \ esid 670 through 680 or (resid 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 693 or (resid 694 through 724 a \ nd (name N or name CA or name C or name O or name CB )) or resid 725 through 733 \ or (resid 734 through 735 and (name N or name CA or name C or name O or name CB \ )) or resid 736 through 742 or (resid 743 through 746 and (name N or name CA or \ name C or name O or name CB )) or resid 747 through 786 or (resid 787 through 7 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 790 through \ 791 or (resid 792 through 793 and (name N or name CA or name C or name O or nam \ e CB )) or resid 794 or (resid 795 through 797 and (name N or name CA or name C \ or name O or name CB )) or resid 798 through 799 or (resid 800 through 806 and ( \ name N or name CA or name C or name O or name CB )) or resid 807 through 808 or \ (resid 809 and (name N or name CA or name C or name O or name CB )) or resid 810 \ or (resid 811 through 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 or (resid 815 through 816 and (name N or name CA or name C or n \ ame O or name CB )) or resid 817 through 819 or (resid 820 and (name N or name C \ A or name C or name O or name CB )) or resid 821 through 858 or (resid 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 864 or \ (resid 865 through 872 and (name N or name CA or name C or name O or name CB )) \ or resid 901 through 902 or resid 904 or resid 905)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.950 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.360 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:15.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.004 0.074 12740 Z= 0.281 Angle : 0.599 12.938 17346 Z= 0.307 Chirality : 0.045 0.272 1991 Planarity : 0.005 0.084 2199 Dihedral : 16.875 88.301 4561 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.08 % Allowed : 29.21 % Favored : 70.71 % 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: -0.13 (0.21), residues: 1590 helix: 1.14 (0.20), residues: 679 sheet: -1.38 (0.36), residues: 203 loop : -0.84 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 299 HIS 0.002 0.000 HIS A 463 PHE 0.015 0.001 PHE B 226 TYR 0.009 0.001 TYR A 421 ARG 0.012 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.399 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 1.0521 time to fit residues: 194.9910 Evaluate side-chains 147 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.8921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12740 Z= 0.357 Angle : 0.573 9.793 17346 Z= 0.300 Chirality : 0.045 0.209 1991 Planarity : 0.004 0.060 2199 Dihedral : 6.823 58.890 1998 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.21 % Allowed : 25.47 % Favored : 69.32 % 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: -0.25 (0.21), residues: 1590 helix: 1.04 (0.19), residues: 700 sheet: -1.57 (0.35), residues: 217 loop : -0.90 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.005 0.001 HIS A 463 PHE 0.018 0.002 PHE B 226 TYR 0.013 0.002 TYR A 421 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 154 time to evaluate : 1.392 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 27 residues processed: 200 average time/residue: 0.9917 time to fit residues: 221.0503 Evaluate side-chains 180 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.6836 time to fit residues: 7.4761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12740 Z= 0.305 Angle : 0.556 9.970 17346 Z= 0.289 Chirality : 0.044 0.202 1991 Planarity : 0.004 0.050 2199 Dihedral : 6.321 57.952 1998 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.13 % Allowed : 24.98 % Favored : 69.89 % 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: -0.20 (0.21), residues: 1590 helix: 1.12 (0.20), residues: 696 sheet: -1.53 (0.35), residues: 212 loop : -0.92 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.021 0.002 PHE B 762 TYR 0.018 0.002 TYR A 435 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 154 time to evaluate : 1.462 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 29 residues processed: 202 average time/residue: 0.9640 time to fit residues: 217.5127 Evaluate side-chains 180 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.6113 time to fit residues: 6.3574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12740 Z= 0.302 Angle : 0.553 9.925 17346 Z= 0.287 Chirality : 0.044 0.205 1991 Planarity : 0.004 0.047 2199 Dihedral : 6.100 56.338 1998 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.29 % Allowed : 24.74 % Favored : 69.98 % 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: -0.18 (0.21), residues: 1590 helix: 1.18 (0.20), residues: 695 sheet: -1.64 (0.34), residues: 218 loop : -0.90 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 299 HIS 0.004 0.001 HIS A 463 PHE 0.021 0.002 PHE A 814 TYR 0.012 0.001 TYR A 421 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 159 time to evaluate : 1.393 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 31 residues processed: 206 average time/residue: 0.9892 time to fit residues: 227.2621 Evaluate side-chains 180 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.3653 time to fit residues: 4.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 459 GLN A 647 ASN A 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 12740 Z= 0.539 Angle : 0.660 10.988 17346 Z= 0.344 Chirality : 0.050 0.249 1991 Planarity : 0.005 0.066 2199 Dihedral : 6.429 55.282 1998 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.18 % Allowed : 24.57 % Favored : 69.24 % 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: -0.42 (0.21), residues: 1590 helix: 0.87 (0.19), residues: 698 sheet: -1.61 (0.35), residues: 206 loop : -0.97 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 299 HIS 0.006 0.001 HIS A 463 PHE 0.027 0.002 PHE A 814 TYR 0.018 0.002 TYR A 421 ARG 0.008 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 156 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 43 residues processed: 215 average time/residue: 0.9926 time to fit residues: 237.9386 Evaluate side-chains 194 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 9 average time/residue: 0.4314 time to fit residues: 6.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN A 357 ASN A 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12740 Z= 0.189 Angle : 0.536 10.175 17346 Z= 0.274 Chirality : 0.043 0.233 1991 Planarity : 0.004 0.046 2199 Dihedral : 5.862 50.180 1998 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.23 % Allowed : 26.36 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1590 helix: 1.25 (0.20), residues: 690 sheet: -1.57 (0.35), residues: 206 loop : -0.86 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 299 HIS 0.002 0.000 HIS A 595 PHE 0.021 0.001 PHE A 814 TYR 0.020 0.001 TYR A 435 ARG 0.006 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 37 residues processed: 191 average time/residue: 1.0514 time to fit residues: 223.5062 Evaluate side-chains 184 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 31 residues processed: 7 average time/residue: 0.6204 time to fit residues: 6.9780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12740 Z= 0.317 Angle : 0.574 10.363 17346 Z= 0.296 Chirality : 0.045 0.239 1991 Planarity : 0.004 0.046 2199 Dihedral : 5.897 50.644 1998 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.64 % Allowed : 26.44 % Favored : 68.92 % 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: -0.19 (0.21), residues: 1590 helix: 1.16 (0.19), residues: 695 sheet: -1.67 (0.34), residues: 218 loop : -0.88 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 299 HIS 0.004 0.001 HIS B 41 PHE 0.025 0.002 PHE A 814 TYR 0.013 0.002 TYR A 421 ARG 0.011 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 1.393 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 197 average time/residue: 0.9781 time to fit residues: 215.5040 Evaluate side-chains 192 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 7 average time/residue: 0.6791 time to fit residues: 7.4043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 121 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: B 124 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12740 Z= 0.370 Angle : 0.600 10.214 17346 Z= 0.310 Chirality : 0.046 0.259 1991 Planarity : 0.004 0.045 2199 Dihedral : 5.980 49.428 1998 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.48 % Allowed : 27.01 % Favored : 68.51 % 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: -0.25 (0.21), residues: 1590 helix: 1.07 (0.19), residues: 696 sheet: -1.61 (0.35), residues: 212 loop : -0.91 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 675 HIS 0.004 0.001 HIS A 463 PHE 0.022 0.002 PHE A 814 TYR 0.013 0.002 TYR A 421 ARG 0.011 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 156 time to evaluate : 1.367 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 41 residues processed: 198 average time/residue: 0.9711 time to fit residues: 214.4147 Evaluate side-chains 193 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 8 average time/residue: 0.2697 time to fit residues: 4.6472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 124 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN A 357 ASN A 753 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12740 Z= 0.218 Angle : 0.557 10.641 17346 Z= 0.283 Chirality : 0.044 0.266 1991 Planarity : 0.004 0.045 2199 Dihedral : 5.673 50.153 1998 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.58 % Allowed : 28.23 % Favored : 68.19 % 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: -0.08 (0.21), residues: 1590 helix: 1.27 (0.20), residues: 691 sheet: -1.66 (0.34), residues: 215 loop : -0.82 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 299 HIS 0.002 0.000 HIS B 41 PHE 0.026 0.001 PHE A 814 TYR 0.010 0.001 TYR B 95 ARG 0.011 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.430 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 35 residues processed: 186 average time/residue: 0.9685 time to fit residues: 202.2043 Evaluate side-chains 183 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 3 average time/residue: 0.1739 time to fit residues: 2.8389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.0170 chunk 146 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 124 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12740 Z= 0.283 Angle : 0.579 9.721 17346 Z= 0.296 Chirality : 0.045 0.278 1991 Planarity : 0.004 0.045 2199 Dihedral : 5.691 49.348 1998 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.74 % Allowed : 28.07 % Favored : 68.19 % 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: -0.15 (0.21), residues: 1590 helix: 1.24 (0.19), residues: 688 sheet: -1.65 (0.34), residues: 217 loop : -0.90 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 675 HIS 0.003 0.001 HIS A 463 PHE 0.020 0.002 PHE A 814 TYR 0.024 0.002 TYR A 435 ARG 0.012 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 1.352 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 36 residues processed: 189 average time/residue: 0.9264 time to fit residues: 196.1717 Evaluate side-chains 187 residues out of total 1402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 5 average time/residue: 0.3714 time to fit residues: 4.2523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118872 restraints weight = 15173.404| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.88 r_work: 0.3244 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12740 Z= 0.318 Angle : 0.594 9.989 17346 Z= 0.304 Chirality : 0.046 0.279 1991 Planarity : 0.004 0.045 2199 Dihedral : 5.750 48.591 1998 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.34 % Allowed : 28.40 % Favored : 68.27 % 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: -0.21 (0.21), residues: 1590 helix: 1.13 (0.19), residues: 693 sheet: -1.65 (0.34), residues: 217 loop : -0.89 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 299 HIS 0.004 0.001 HIS B 41 PHE 0.034 0.002 PHE A 814 TYR 0.012 0.002 TYR A 421 ARG 0.012 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4505.27 seconds wall clock time: 83 minutes 44.36 seconds (5024.36 seconds total)