Starting phenix.real_space_refine on Sat Nov 18 12:50:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sur_40776/11_2023/8sur_40776_trim.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.015 sd= 0.827 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 71 5.16 5 C 7697 2.51 5 N 1866 2.21 5 O 2065 1.98 5 H 11381 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 72": "OD1" <-> "OD2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 859": "OD1" <-> "OD2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 767": "OD1" <-> "OD2" Residue "B TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 774": "OD1" <-> "OD2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 859": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 23085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 11021 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 11919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 11919 Classifications: {'peptide': 726} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 693} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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 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 chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' CA': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.62, per 1000 atoms: 0.42 Number of scatterers: 23085 At special positions: 0 Unit cell: (134.24, 90.612, 125.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 71 16.00 O 2065 8.00 N 1866 7.00 C 7697 6.00 H 11381 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=1.93 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " 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-ASN " NAG A 901 " - " ASN A 362 " " NAG A 902 " - " ASN A 785 " " NAG A 904 " - " ASN A 778 " Time building additional restraints: 17.08 Conformation dependent library (CDL) restraints added in 2.2 seconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 64.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.931A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.709A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.946A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.827A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 540 removed outlier: 3.834A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.666A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 removed outlier: 3.537A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 638 removed outlier: 3.851A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.796A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.058A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.122A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'B' and resid 87 through 109 removed outlier: 4.032A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.959A pdb=" N ARG B 191 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.641A pdb=" N PHE B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 204' Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.885A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.561A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.832A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 488 Processing helix chain 'B' and resid 504 through 539 removed outlier: 4.157A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.582A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 removed outlier: 4.096A pdb=" N GLN B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.763A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.090A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.040A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.593A pdb=" N ILE B 868 " --> pdb=" O THR B 864 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.744A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.904A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.436A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.996A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 784 through 785 685 hydrogen bonds defined for protein. 2016 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: 7.86 Time building geometry restraints manager: 17.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10867 1.04 - 1.23: 948 1.23 - 1.43: 4824 1.43 - 1.63: 6655 1.63 - 1.83: 112 Bond restraints: 23406 Sorted by residual: bond pdb=" C TRP A 359 " pdb=" O TRP A 359 " ideal model delta sigma weight residual 1.236 1.052 0.184 1.19e-02 7.06e+03 2.38e+02 bond pdb=" C CYS A 349 " pdb=" O CYS A 349 " ideal model delta sigma weight residual 1.236 1.090 0.145 1.00e-02 1.00e+04 2.11e+02 bond pdb=" C ARG A 360 " pdb=" O ARG A 360 " ideal model delta sigma weight residual 1.233 1.052 0.181 1.57e-02 4.06e+03 1.33e+02 bond pdb=" C GLU B 405 " pdb=" O GLU B 405 " ideal model delta sigma weight residual 1.237 1.104 0.132 1.17e-02 7.31e+03 1.28e+02 bond pdb=" CA GLN B 506 " pdb=" C GLN B 506 " ideal model delta sigma weight residual 1.523 1.387 0.136 1.41e-02 5.03e+03 9.31e+01 ... (remaining 23401 not shown) Histogram of bond angle deviations from ideal: 73.44 - 85.56: 23 85.56 - 97.69: 5 97.69 - 109.82: 17264 109.82 - 121.94: 21199 121.94 - 134.07: 3654 Bond angle restraints: 42145 Sorted by residual: angle pdb=" C CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sigma weight residual 111.00 123.03 -12.03 8.70e-01 1.32e+00 1.91e+02 angle pdb=" C GLU B 405 " pdb=" CA GLU B 405 " pdb=" CB GLU B 405 " ideal model delta sigma weight residual 110.79 88.84 21.95 1.66e+00 3.63e-01 1.75e+02 angle pdb=" C SER A 278 " pdb=" CA SER A 278 " pdb=" HA SER A 278 " ideal model delta sigma weight residual 109.00 73.44 35.56 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.50 35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 ... (remaining 42140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8595 17.77 - 35.53: 743 35.53 - 53.30: 129 53.30 - 71.07: 32 71.07 - 88.83: 14 Dihedral angle restraints: 9513 sinusoidal: 4212 harmonic: 5301 Sorted by residual: dihedral pdb=" C CYS A 356 " pdb=" N CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta harmonic sigma weight residual -122.60 -163.73 41.13 0 2.50e+00 1.60e-01 2.71e+02 dihedral pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta harmonic sigma weight residual 122.80 163.01 -40.21 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" C GLU B 405 " pdb=" N GLU B 405 " pdb=" CA GLU B 405 " pdb=" CB GLU B 405 " ideal model delta harmonic sigma weight residual -122.60 -100.11 -22.49 0 2.50e+00 1.60e-01 8.09e+01 ... (remaining 9510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1794 0.345 - 0.691: 6 0.691 - 1.036: 0 1.036 - 1.382: 1 1.382 - 1.727: 2 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.46e+01 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.00e+01 chirality pdb=" C3 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C4 NAG D 2 " pdb=" O3 NAG D 2 " both_signs ideal model delta sigma weight residual False 2.45 1.11 1.34 2.00e-01 2.50e+01 4.50e+01 ... (remaining 1800 not shown) Planarity restraints: 3361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 401 " -0.061 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C GLN B 401 " 0.194 2.00e-02 2.50e+03 pdb=" O GLN B 401 " -0.067 2.00e-02 2.50e+03 pdb=" N ALA B 402 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 359 " 0.036 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" C TRP A 359 " -0.128 2.00e-02 2.50e+03 pdb=" O TRP A 359 " 0.046 2.00e-02 2.50e+03 pdb=" N ARG A 360 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 359 " 0.069 2.00e-02 2.50e+03 3.46e-02 4.78e+01 pdb=" CG TRP A 359 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 TRP A 359 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 359 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 359 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 359 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 359 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 359 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 359 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 359 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A 359 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 359 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 359 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 359 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 359 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 359 " 0.001 2.00e-02 2.50e+03 ... (remaining 3358 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.92: 66 1.92 - 2.59: 23702 2.59 - 3.26: 70082 3.26 - 3.93: 83997 3.93 - 4.60: 131261 Nonbonded interactions: 309108 Sorted by model distance: nonbonded pdb=" OD1 ASP B 859 " pdb="CA CA B 904 " model vdw 1.256 2.390 nonbonded pdb=" OE2 GLU B 624 " pdb="CA CA B 902 " model vdw 1.365 2.390 nonbonded pdb=" H SER A 278 " pdb=" HA SER A 278 " model vdw 1.595 1.816 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.598 1.952 nonbonded pdb=" O GLY A 344 " pdb=" HE ARG A 360 " model vdw 1.605 1.850 ... (remaining 309103 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 59 through 868 or resid 904 or resid 906 through 907)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 409 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 777 or ( \ resid 778 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 868 or resid 901 or resid 903 through 904)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.320 Extract box with map and model: 4.870 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 67.910 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.007 0.184 12025 Z= 0.486 Angle : 0.853 21.948 16320 Z= 0.552 Chirality : 0.082 1.727 1803 Planarity : 0.006 0.112 2015 Dihedral : 13.775 87.004 4268 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.94 % Favored : 95.70 % Rotamer: Outliers : 0.65 % Allowed : 0.32 % Favored : 99.03 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1395 helix: 2.00 (0.17), residues: 833 sheet: -0.47 (0.66), residues: 63 loop : -1.49 (0.27), residues: 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 221 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 227 average time/residue: 0.4834 time to fit residues: 160.5605 Evaluate side-chains 172 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2696 time to fit residues: 3.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.0270 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12025 Z= 0.170 Angle : 0.535 7.726 16320 Z= 0.290 Chirality : 0.045 0.407 1803 Planarity : 0.005 0.062 2015 Dihedral : 3.641 17.212 1561 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 0.41 % Allowed : 4.46 % Favored : 95.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1395 helix: 2.21 (0.17), residues: 839 sheet: -0.25 (0.75), residues: 53 loop : -1.52 (0.26), residues: 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 180 average time/residue: 0.4564 time to fit residues: 123.0270 Evaluate side-chains 168 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2569 time to fit residues: 4.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12025 Z= 0.304 Angle : 0.574 9.590 16320 Z= 0.315 Chirality : 0.048 0.437 1803 Planarity : 0.005 0.049 2015 Dihedral : 3.904 16.596 1561 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 0.65 % Allowed : 6.66 % Favored : 92.69 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1395 helix: 2.07 (0.17), residues: 827 sheet: -1.39 (0.58), residues: 72 loop : -1.53 (0.26), residues: 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 190 average time/residue: 0.4507 time to fit residues: 130.4661 Evaluate side-chains 172 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2572 time to fit residues: 5.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12025 Z= 0.166 Angle : 0.502 7.929 16320 Z= 0.272 Chirality : 0.045 0.415 1803 Planarity : 0.004 0.075 2015 Dihedral : 3.763 16.086 1561 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.08 % Favored : 96.70 % Rotamer: Outliers : 0.49 % Allowed : 8.69 % Favored : 90.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1395 helix: 2.22 (0.17), residues: 840 sheet: -1.45 (0.57), residues: 74 loop : -1.44 (0.26), residues: 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 173 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 176 average time/residue: 0.4657 time to fit residues: 122.7930 Evaluate side-chains 166 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2720 time to fit residues: 4.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12025 Z= 0.215 Angle : 0.511 8.270 16320 Z= 0.277 Chirality : 0.045 0.425 1803 Planarity : 0.004 0.058 2015 Dihedral : 3.763 15.886 1561 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.99 % Rotamer: Outliers : 0.57 % Allowed : 8.85 % Favored : 90.58 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1395 helix: 2.27 (0.17), residues: 829 sheet: -1.40 (0.58), residues: 74 loop : -1.40 (0.26), residues: 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.4495 time to fit residues: 116.9729 Evaluate side-chains 164 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2758 time to fit residues: 5.2847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12025 Z= 0.221 Angle : 0.516 7.974 16320 Z= 0.279 Chirality : 0.045 0.428 1803 Planarity : 0.004 0.057 2015 Dihedral : 3.782 17.157 1561 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.51 % Favored : 96.27 % Rotamer: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1395 helix: 2.26 (0.17), residues: 835 sheet: -1.43 (0.59), residues: 74 loop : -1.36 (0.27), residues: 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 171 average time/residue: 0.4625 time to fit residues: 120.9512 Evaluate side-chains 159 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2494 time to fit residues: 3.1391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12025 Z= 0.236 Angle : 0.522 8.047 16320 Z= 0.283 Chirality : 0.046 0.426 1803 Planarity : 0.004 0.051 2015 Dihedral : 3.800 16.776 1561 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.65 % Allowed : 10.06 % Favored : 89.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1395 helix: 2.29 (0.17), residues: 825 sheet: -1.40 (0.59), residues: 76 loop : -1.38 (0.26), residues: 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 166 average time/residue: 0.4329 time to fit residues: 110.2538 Evaluate side-chains 167 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2546 time to fit residues: 5.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12025 Z= 0.201 Angle : 0.509 7.864 16320 Z= 0.274 Chirality : 0.045 0.416 1803 Planarity : 0.004 0.054 2015 Dihedral : 3.779 17.260 1561 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.30 % Favored : 96.49 % Rotamer: Outliers : 0.32 % Allowed : 10.47 % Favored : 89.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1395 helix: 2.35 (0.17), residues: 825 sheet: -1.36 (0.58), residues: 76 loop : -1.33 (0.27), residues: 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 171 average time/residue: 0.4452 time to fit residues: 116.2711 Evaluate side-chains 167 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2837 time to fit residues: 4.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12025 Z= 0.160 Angle : 0.499 7.812 16320 Z= 0.267 Chirality : 0.044 0.431 1803 Planarity : 0.004 0.049 2015 Dihedral : 3.702 16.551 1561 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.51 % Favored : 96.27 % Rotamer: Outliers : 0.16 % Allowed : 10.80 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1395 helix: 2.46 (0.17), residues: 825 sheet: -1.24 (0.59), residues: 76 loop : -1.27 (0.27), residues: 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 171 average time/residue: 0.4419 time to fit residues: 115.1080 Evaluate side-chains 164 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2519 time to fit residues: 3.3071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12025 Z= 0.344 Angle : 0.567 8.044 16320 Z= 0.309 Chirality : 0.047 0.415 1803 Planarity : 0.005 0.052 2015 Dihedral : 3.916 17.431 1561 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.77 % Rotamer: Outliers : 0.24 % Allowed : 11.20 % Favored : 88.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1395 helix: 2.17 (0.17), residues: 824 sheet: -1.48 (0.59), residues: 77 loop : -1.52 (0.26), residues: 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 167 average time/residue: 0.4459 time to fit residues: 113.3094 Evaluate side-chains 167 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2822 time to fit residues: 3.3391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 115 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 0.0870 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.150644 restraints weight = 40828.941| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.38 r_work: 0.3672 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12025 Z= 0.198 Angle : 0.520 7.869 16320 Z= 0.280 Chirality : 0.045 0.425 1803 Planarity : 0.004 0.049 2015 Dihedral : 3.844 17.176 1561 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer: Outliers : 0.32 % Allowed : 11.53 % Favored : 88.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1395 helix: 2.27 (0.17), residues: 831 sheet: -1.42 (0.59), residues: 76 loop : -1.41 (0.27), residues: 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4987.46 seconds wall clock time: 89 minutes 15.41 seconds (5355.41 seconds total)