Starting phenix.real_space_refine on Thu Sep 18 03:32:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hlw_52273/09_2025/9hlw_52273.map" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.022 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 2 9.91 5 Zn 4 6.06 5 S 48 5.16 5 Cl 1 4.86 5 C 8519 2.51 5 N 2208 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13375 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 690, 5504 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 690, 5504 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645} Chain breaks: 2 bond proxies already assigned to first conformer: 5634 Chain: "E" Number of atoms: 5545 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 690, 5504 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 690, 5504 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645} Chain breaks: 2 bond proxies already assigned to first conformer: 5612 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 965 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Q" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 965 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 60 Unusual residues: {' CA': 1, ' CL': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AGLU A 183 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 183 " occ=0.50 residue: pdb=" N ASER A 613 " occ=0.70 ... (10 atoms not shown) pdb=" OG BSER A 613 " occ=0.30 residue: pdb=" N AGLN E 79 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN E 79 " occ=0.50 residue: pdb=" N ASER E 155 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 155 " occ=0.50 residue: pdb=" N AGLU E 183 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU E 183 " occ=0.50 residue: pdb=" N ASER E 613 " occ=0.70 ... (10 atoms not shown) pdb=" OG BSER E 613 " occ=0.30 residue: pdb=" N AVAL E 660 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL E 660 " occ=0.50 Time building chain proxies: 6.21, per 1000 atoms: 0.46 Number of scatterers: 13375 At special positions: 0 Unit cell: (107.69, 126.38, 91.67, 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) Zn 4 29.99 Ca 2 19.99 Cl 1 17.00 S 48 16.00 O 2593 8.00 N 2208 7.00 C 8519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 801 " - " ASN A 121 " " NAG A 802 " - " ASN A 140 " " NAG A 804 " - " ASN A 459 " " NAG E 801 " - " ASN E 121 " " NAG E 802 " - " ASN E 140 " " NAG E 804 " - " ASN E 459 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 553 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 377 " pdb=" ZN E 805 " pdb="ZN ZN E 805 " - pdb=" NE2 HIS E 553 " pdb=" ZN E 806 " pdb="ZN ZN E 806 " - pdb=" NE2 HIS E 377 " 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 35.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.653A pdb=" N PHE A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.523A pdb=" N ILE A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 388 through 409 removed outlier: 4.045A pdb=" N VAL A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.714A pdb=" N LYS A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.508A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'A' and resid 558 through 566 removed outlier: 3.546A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 590 Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.775A pdb=" N TYR A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 629 through 653 Processing helix chain 'A' and resid 657 through 670 removed outlier: 3.810A pdb=" N MET A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 720 through 746 removed outlier: 3.839A pdb=" N LEU A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.625A pdb=" N PHE E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.569A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.639A pdb=" N ASP E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 230 through 235 Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 388 through 409 removed outlier: 4.072A pdb=" N VAL E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 438 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 470 through 479 removed outlier: 3.664A pdb=" N LYS E 479 " --> pdb=" O HIS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 558 through 566 removed outlier: 3.531A pdb=" N VAL E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 590 Processing helix chain 'E' and resid 596 through 617 removed outlier: 3.812A pdb=" N TYR E 600 " --> pdb=" O ASP E 596 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 602 " --> pdb=" O ARG E 598 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 603 " --> pdb=" O ASP E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 629 through 653 Processing helix chain 'E' and resid 657 through 670 Processing helix chain 'E' and resid 671 through 676 Processing helix chain 'E' and resid 705 through 712 Processing helix chain 'E' and resid 720 through 746 removed outlier: 3.834A pdb=" N LEU E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 Processing helix chain 'Q' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 119 removed outlier: 3.781A pdb=" N SER A 107 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 415 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 370 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 417 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 372 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA A 419 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 374 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TRP A 421 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY A 376 " --> pdb=" O TRP A 421 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N GLY A 446 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N ASP A 369 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N ALA A 448 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR A 371 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 450 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A 373 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 531 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 535 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 204 removed outlier: 7.229A pdb=" N VAL A 225 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ILE A 297 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 227 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 107 through 119 removed outlier: 3.798A pdb=" N SER E 107 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR E 415 " --> pdb=" O PRO E 368 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG E 370 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 417 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 372 " --> pdb=" O LEU E 417 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA E 419 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU E 374 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP E 421 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY E 376 " --> pdb=" O TRP E 421 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLY E 446 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N ASP E 369 " --> pdb=" O GLY E 446 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ALA E 448 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR E 371 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE E 450 " --> pdb=" O TYR E 371 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 373 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA E 531 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA E 535 " --> pdb=" O ASN E 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 140 removed outlier: 3.630A pdb=" N PHE E 139 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 162 through 163 Processing sheet with id=AA8, first strand: chain 'E' and resid 174 through 176 removed outlier: 6.561A pdb=" N VAL E 175 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ARG E 204 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL E 225 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE E 297 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 227 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.028A pdb=" N VAL H 12 " --> pdb=" O VAL H 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 31 through 32 removed outlier: 3.785A pdb=" N ASN H 31 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.123A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL H 98 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU H 116 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'Q' and resid 31 through 32 removed outlier: 3.791A pdb=" N ASN Q 31 " --> pdb=" O CYS Q 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 57 through 60 removed outlier: 6.838A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1455 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: 2.50 Time building geometry restraints manager: 1.74 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: 4258 1.34 - 1.46: 3081 1.46 - 1.58: 6305 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 13726 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.32e+00 bond pdb=" C1 NAG E 803 " pdb=" O5 NAG E 803 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 MAN I 5 " pdb=" C2 MAN I 5 " ideal model delta sigma weight residual 1.526 1.559 -0.033 2.00e-02 2.50e+03 2.78e+00 ... (remaining 13721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 18380 2.73 - 5.47: 206 5.47 - 8.20: 24 8.20 - 10.94: 5 10.94 - 13.67: 4 Bond angle restraints: 18619 Sorted by residual: angle pdb=" CA LEU Q 116 " pdb=" CB LEU Q 116 " pdb=" CG LEU Q 116 " ideal model delta sigma weight residual 116.30 129.97 -13.67 3.50e+00 8.16e-02 1.53e+01 angle pdb=" CA LEU H 81 " pdb=" CB LEU H 81 " pdb=" CG LEU H 81 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 angle pdb=" CA GLU A 102 " pdb=" CB GLU A 102 " pdb=" CG GLU A 102 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA LEU H 116 " pdb=" CB LEU H 116 " pdb=" CG LEU H 116 " ideal model delta sigma weight residual 116.30 128.93 -12.63 3.50e+00 8.16e-02 1.30e+01 angle pdb=" CA ARG A 190 " pdb=" CB ARG A 190 " pdb=" CG ARG A 190 " ideal model delta sigma weight residual 114.10 120.86 -6.76 2.00e+00 2.50e-01 1.14e+01 ... (remaining 18614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 7953 25.69 - 51.39: 426 51.39 - 77.08: 66 77.08 - 102.78: 32 102.78 - 128.47: 20 Dihedral angle restraints: 8497 sinusoidal: 3755 harmonic: 4742 Sorted by residual: dihedral pdb=" C2 NAG B 1 " pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " pdb=" C5 NAG B 1 " ideal model delta sinusoidal sigma weight residual -62.96 65.51 -128.47 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG E 803 " pdb=" C1 NAG E 803 " pdb=" O5 NAG E 803 " pdb=" C5 NAG E 803 " ideal model delta sinusoidal sigma weight residual -62.96 64.90 -127.86 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sinusoidal sigma weight residual -62.96 62.72 -125.68 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 8494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1681 0.058 - 0.117: 310 0.117 - 0.175: 23 0.175 - 0.234: 1 0.234 - 0.292: 4 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2016 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 714 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ASP E 714 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP E 714 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE E 715 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 387 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A 388 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 387 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO E 388 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 388 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 388 " -0.025 5.00e-02 4.00e+02 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 188 2.57 - 3.16: 11264 3.16 - 3.74: 22023 3.74 - 4.32: 31439 4.32 - 4.90: 50756 Nonbonded interactions: 115670 Sorted by model distance: nonbonded pdb=" OE2 GLU A 425 " pdb="ZN ZN A 805 " model vdw 1.993 2.230 nonbonded pdb=" OE2 GLU E 425 " pdb="ZN ZN E 805 " model vdw 1.995 2.230 nonbonded pdb=" OD1 ASP E 387 " pdb="ZN ZN E 806 " model vdw 2.038 2.230 nonbonded pdb=" OD1 ASP A 387 " pdb="ZN ZN A 806 " model vdw 2.039 2.230 nonbonded pdb=" OG ASER E 613 " pdb=" O ALA H 100 " model vdw 2.110 3.040 ... (remaining 115665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 78 or resid 80 through 154 or resid 156 through \ 182 or resid 184 through 525 or resid 527 through 612 or resid 614 through 659 \ or resid 661 through 807)) selection = (chain 'E' and (resid 56 through 78 or resid 80 through 154 or resid 156 through \ 182 or resid 184 through 525 or resid 527 through 612 or resid 614 through 659 \ or resid 661 through 807)) } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'Q' } 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=0.30 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: 1.180 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.190 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.047 13754 Z= 0.176 Angle : 0.719 13.673 18687 Z= 0.339 Chirality : 0.046 0.292 2019 Planarity : 0.004 0.050 2394 Dihedral : 17.568 128.474 5473 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.29 % Allowed : 21.22 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1638 helix: 1.41 (0.23), residues: 520 sheet: -0.23 (0.31), residues: 284 loop : -0.53 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 190 TYR 0.011 0.001 TYR E 299 PHE 0.028 0.001 PHE Q 68 TRP 0.033 0.002 TRP A 410 HIS 0.007 0.001 HIS A 697 Details of bonding type rmsd covalent geometry : bond 0.00381 (13726) covalent geometry : angle 0.71525 (18619) SS BOND : bond 0.00389 ( 4) SS BOND : angle 0.41532 ( 8) hydrogen bonds : bond 0.15703 ( 508) hydrogen bonds : angle 6.49536 ( 1455) metal coordination : bond 0.00323 ( 4) link_ALPHA1-3 : bond 0.00270 ( 2) link_ALPHA1-3 : angle 1.95750 ( 6) link_ALPHA1-6 : bond 0.00431 ( 2) link_ALPHA1-6 : angle 1.64539 ( 6) link_BETA1-4 : bond 0.00252 ( 10) link_BETA1-4 : angle 1.53850 ( 30) link_NAG-ASN : bond 0.00209 ( 6) link_NAG-ASN : angle 1.19674 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8187 (mtt-85) REVERT: Q 5 GLN cc_start: 0.9158 (mp10) cc_final: 0.8942 (mp10) outliers start: 18 outliers final: 16 residues processed: 162 average time/residue: 0.5577 time to fit residues: 100.2736 Evaluate side-chains 156 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 517 SER Chi-restraints excluded: chain E residue 575 THR Chi-restraints excluded: chain E residue 627 VAL Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain Q residue 110 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 260 ASN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106972 restraints weight = 81894.351| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 5.46 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13754 Z= 0.119 Angle : 0.665 11.219 18687 Z= 0.319 Chirality : 0.043 0.228 2019 Planarity : 0.004 0.052 2394 Dihedral : 12.246 96.408 2407 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.15 % Allowed : 18.14 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.21), residues: 1638 helix: 1.56 (0.23), residues: 518 sheet: -0.09 (0.33), residues: 244 loop : -0.49 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 67 TYR 0.024 0.001 TYR Q 114 PHE 0.016 0.001 PHE A 186 TRP 0.020 0.001 TRP E 410 HIS 0.007 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00263 (13726) covalent geometry : angle 0.65723 (18619) SS BOND : bond 0.00431 ( 4) SS BOND : angle 0.55106 ( 8) hydrogen bonds : bond 0.04305 ( 508) hydrogen bonds : angle 5.17614 ( 1455) metal coordination : bond 0.00099 ( 4) link_ALPHA1-3 : bond 0.00984 ( 2) link_ALPHA1-3 : angle 2.06260 ( 6) link_ALPHA1-6 : bond 0.00823 ( 2) link_ALPHA1-6 : angle 2.58483 ( 6) link_BETA1-4 : bond 0.00385 ( 10) link_BETA1-4 : angle 1.95722 ( 30) link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.32891 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 714 ASP cc_start: 0.7482 (t70) cc_final: 0.7246 (t0) REVERT: H 79 MET cc_start: 0.6816 (mpt) cc_final: 0.6287 (mpt) REVERT: Q 5 GLN cc_start: 0.9219 (mp10) cc_final: 0.8939 (mp10) REVERT: Q 87 LYS cc_start: 0.8160 (mppt) cc_final: 0.7951 (mppt) outliers start: 29 outliers final: 11 residues processed: 169 average time/residue: 0.6303 time to fit residues: 116.7089 Evaluate side-chains 152 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 575 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 618 HIS A 638 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.132907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106146 restraints weight = 89817.191| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 5.70 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13754 Z= 0.126 Angle : 0.631 10.702 18687 Z= 0.306 Chirality : 0.043 0.158 2019 Planarity : 0.004 0.048 2394 Dihedral : 8.054 81.298 2389 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.08 % Allowed : 18.06 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.20), residues: 1638 helix: 1.49 (0.23), residues: 530 sheet: -0.21 (0.32), residues: 268 loop : -0.57 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.016 0.001 TYR E 299 PHE 0.020 0.001 PHE A 337 TRP 0.026 0.001 TRP E 410 HIS 0.007 0.001 HIS A 475 Details of bonding type rmsd covalent geometry : bond 0.00287 (13726) covalent geometry : angle 0.62486 (18619) SS BOND : bond 0.00363 ( 4) SS BOND : angle 0.57425 ( 8) hydrogen bonds : bond 0.04133 ( 508) hydrogen bonds : angle 5.02798 ( 1455) metal coordination : bond 0.00282 ( 4) link_ALPHA1-3 : bond 0.00903 ( 2) link_ALPHA1-3 : angle 1.49984 ( 6) link_ALPHA1-6 : bond 0.00785 ( 2) link_ALPHA1-6 : angle 1.73327 ( 6) link_BETA1-4 : bond 0.00441 ( 10) link_BETA1-4 : angle 1.92726 ( 30) link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 1.29806 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8456 (t80) cc_final: 0.8123 (t80) REVERT: A 190 ARG cc_start: 0.8930 (mmt180) cc_final: 0.8693 (ppt170) REVERT: A 522 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: A 537 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: A 714 ASP cc_start: 0.7385 (t70) cc_final: 0.6804 (t70) REVERT: E 536 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7737 (ptp90) REVERT: E 616 MET cc_start: 0.7949 (mmm) cc_final: 0.7690 (tpp) REVERT: H 44 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8742 (mp0) REVERT: H 79 MET cc_start: 0.6984 (mpt) cc_final: 0.6294 (mpt) REVERT: Q 5 GLN cc_start: 0.9240 (mp10) cc_final: 0.8928 (mp10) outliers start: 28 outliers final: 11 residues processed: 164 average time/residue: 0.6528 time to fit residues: 117.1803 Evaluate side-chains 147 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 78 optimal weight: 0.0040 chunk 156 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS A 475 HIS A 638 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.130853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.105106 restraints weight = 74614.357| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 5.17 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13754 Z= 0.170 Angle : 0.647 12.038 18687 Z= 0.316 Chirality : 0.044 0.144 2019 Planarity : 0.004 0.047 2394 Dihedral : 6.222 81.622 2388 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 18.57 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1638 helix: 1.44 (0.23), residues: 530 sheet: -0.40 (0.31), residues: 284 loop : -0.57 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 649 TYR 0.019 0.001 TYR Q 114 PHE 0.015 0.001 PHE A 337 TRP 0.025 0.001 TRP A 410 HIS 0.006 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00401 (13726) covalent geometry : angle 0.64121 (18619) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.66892 ( 8) hydrogen bonds : bond 0.04595 ( 508) hydrogen bonds : angle 5.03410 ( 1455) metal coordination : bond 0.00571 ( 4) link_ALPHA1-3 : bond 0.00945 ( 2) link_ALPHA1-3 : angle 1.50664 ( 6) link_ALPHA1-6 : bond 0.00639 ( 2) link_ALPHA1-6 : angle 1.86865 ( 6) link_BETA1-4 : bond 0.00410 ( 10) link_BETA1-4 : angle 1.80718 ( 30) link_NAG-ASN : bond 0.00211 ( 6) link_NAG-ASN : angle 1.34919 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8459 (t80) cc_final: 0.7227 (t80) REVERT: A 190 ARG cc_start: 0.8913 (mmt180) cc_final: 0.8706 (ptt90) REVERT: A 537 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 714 ASP cc_start: 0.7211 (t70) cc_final: 0.6890 (t70) REVERT: E 307 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: E 537 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: E 714 ASP cc_start: 0.6909 (t70) cc_final: 0.6572 (t70) REVERT: H 44 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8772 (mp0) REVERT: H 79 MET cc_start: 0.7043 (mpt) cc_final: 0.6371 (mpt) REVERT: Q 5 GLN cc_start: 0.9251 (mp10) cc_final: 0.8966 (mp10) outliers start: 29 outliers final: 9 residues processed: 160 average time/residue: 0.6199 time to fit residues: 109.0336 Evaluate side-chains 145 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 544 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Q 1 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.132647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.106855 restraints weight = 81489.548| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 5.44 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13754 Z= 0.117 Angle : 0.624 12.096 18687 Z= 0.303 Chirality : 0.042 0.146 2019 Planarity : 0.004 0.049 2394 Dihedral : 5.938 82.031 2386 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.29 % Allowed : 18.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.21), residues: 1638 helix: 1.66 (0.23), residues: 522 sheet: -0.42 (0.30), residues: 304 loop : -0.47 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 190 TYR 0.015 0.001 TYR A 299 PHE 0.015 0.001 PHE A 333 TRP 0.029 0.001 TRP E 410 HIS 0.005 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00274 (13726) covalent geometry : angle 0.61837 (18619) SS BOND : bond 0.00391 ( 4) SS BOND : angle 0.50593 ( 8) hydrogen bonds : bond 0.03942 ( 508) hydrogen bonds : angle 4.89903 ( 1455) metal coordination : bond 0.00188 ( 4) link_ALPHA1-3 : bond 0.00886 ( 2) link_ALPHA1-3 : angle 1.53346 ( 6) link_ALPHA1-6 : bond 0.00334 ( 2) link_ALPHA1-6 : angle 1.55301 ( 6) link_BETA1-4 : bond 0.00375 ( 10) link_BETA1-4 : angle 1.69927 ( 30) link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 1.32684 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8480 (t80) cc_final: 0.8170 (t80) REVERT: A 537 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: A 714 ASP cc_start: 0.7306 (t70) cc_final: 0.6732 (t70) REVERT: E 307 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: E 536 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7797 (ptp90) REVERT: E 714 ASP cc_start: 0.6905 (t70) cc_final: 0.6500 (t70) REVERT: H 44 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: H 79 MET cc_start: 0.7071 (mpt) cc_final: 0.6356 (mpt) REVERT: Q 5 GLN cc_start: 0.9213 (mp10) cc_final: 0.8928 (mp10) REVERT: Q 44 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8827 (mp0) outliers start: 31 outliers final: 12 residues processed: 166 average time/residue: 0.6354 time to fit residues: 115.9086 Evaluate side-chains 147 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.0670 chunk 137 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 0.0370 chunk 128 optimal weight: 0.8980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.133179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107465 restraints weight = 77625.737| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 5.33 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13754 Z= 0.114 Angle : 0.616 12.141 18687 Z= 0.298 Chirality : 0.042 0.151 2019 Planarity : 0.004 0.048 2394 Dihedral : 5.721 82.237 2386 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.01 % Allowed : 18.85 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1638 helix: 1.74 (0.23), residues: 522 sheet: -0.29 (0.31), residues: 294 loop : -0.49 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 190 TYR 0.019 0.001 TYR Q 114 PHE 0.014 0.001 PHE Q 68 TRP 0.037 0.001 TRP E 410 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00268 (13726) covalent geometry : angle 0.61132 (18619) SS BOND : bond 0.00459 ( 4) SS BOND : angle 0.52769 ( 8) hydrogen bonds : bond 0.03735 ( 508) hydrogen bonds : angle 4.80780 ( 1455) metal coordination : bond 0.00212 ( 4) link_ALPHA1-3 : bond 0.00869 ( 2) link_ALPHA1-3 : angle 1.40430 ( 6) link_ALPHA1-6 : bond 0.00322 ( 2) link_ALPHA1-6 : angle 1.53054 ( 6) link_BETA1-4 : bond 0.00370 ( 10) link_BETA1-4 : angle 1.61073 ( 30) link_NAG-ASN : bond 0.00279 ( 6) link_NAG-ASN : angle 1.30265 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 186 PHE cc_start: 0.8476 (t80) cc_final: 0.8215 (t80) REVERT: A 537 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 714 ASP cc_start: 0.7383 (t70) cc_final: 0.6816 (t70) REVERT: E 307 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: E 536 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7822 (ptp90) REVERT: E 616 MET cc_start: 0.8107 (mmm) cc_final: 0.7851 (tpp) REVERT: E 714 ASP cc_start: 0.6967 (t70) cc_final: 0.6510 (t70) REVERT: H 44 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8733 (mp0) REVERT: H 79 MET cc_start: 0.7115 (mpt) cc_final: 0.6339 (mpt) REVERT: Q 5 GLN cc_start: 0.9277 (mp10) cc_final: 0.9001 (mp10) REVERT: Q 46 GLU cc_start: 0.8725 (tt0) cc_final: 0.8415 (pt0) REVERT: Q 81 LEU cc_start: 0.6865 (mp) cc_final: 0.6637 (mp) REVERT: Q 87 LYS cc_start: 0.8288 (mppt) cc_final: 0.8048 (mppt) outliers start: 27 outliers final: 12 residues processed: 155 average time/residue: 0.6575 time to fit residues: 111.9809 Evaluate side-chains 145 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 113 optimal weight: 0.0870 chunk 160 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 122 optimal weight: 0.0980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.134964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.108277 restraints weight = 85244.861| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 5.69 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13754 Z= 0.105 Angle : 0.607 12.029 18687 Z= 0.294 Chirality : 0.041 0.182 2019 Planarity : 0.004 0.050 2394 Dihedral : 5.529 82.011 2386 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.72 % Allowed : 19.43 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1638 helix: 1.78 (0.23), residues: 524 sheet: -0.11 (0.31), residues: 290 loop : -0.48 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 190 TYR 0.016 0.001 TYR E 299 PHE 0.020 0.001 PHE A 337 TRP 0.032 0.001 TRP A 410 HIS 0.005 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00243 (13726) covalent geometry : angle 0.60290 (18619) SS BOND : bond 0.00497 ( 4) SS BOND : angle 0.51384 ( 8) hydrogen bonds : bond 0.03409 ( 508) hydrogen bonds : angle 4.71356 ( 1455) metal coordination : bond 0.00098 ( 4) link_ALPHA1-3 : bond 0.00784 ( 2) link_ALPHA1-3 : angle 1.40356 ( 6) link_ALPHA1-6 : bond 0.00362 ( 2) link_ALPHA1-6 : angle 1.50468 ( 6) link_BETA1-4 : bond 0.00374 ( 10) link_BETA1-4 : angle 1.54519 ( 30) link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 1.27531 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8316 (mp0) cc_final: 0.8095 (mp0) REVERT: A 537 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: A 714 ASP cc_start: 0.7390 (t70) cc_final: 0.6805 (t70) REVERT: E 307 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: E 536 ARG cc_start: 0.8124 (ptp90) cc_final: 0.7775 (ptp90) REVERT: E 560 GLU cc_start: 0.8234 (mp0) cc_final: 0.7651 (mp0) REVERT: E 714 ASP cc_start: 0.7043 (t70) cc_final: 0.6582 (t70) REVERT: H 44 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8711 (mp0) REVERT: H 79 MET cc_start: 0.7158 (mpt) cc_final: 0.6344 (mpt) REVERT: Q 5 GLN cc_start: 0.9237 (mp10) cc_final: 0.8963 (mp10) REVERT: Q 46 GLU cc_start: 0.8704 (tt0) cc_final: 0.8417 (pt0) REVERT: Q 81 LEU cc_start: 0.6770 (mp) cc_final: 0.6457 (mp) outliers start: 23 outliers final: 11 residues processed: 153 average time/residue: 0.6575 time to fit residues: 110.4893 Evaluate side-chains 146 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 307 GLU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 118 optimal weight: 0.0970 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 92 optimal weight: 0.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.133623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.106955 restraints weight = 77827.501| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 5.38 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13754 Z= 0.126 Angle : 0.628 12.683 18687 Z= 0.305 Chirality : 0.042 0.159 2019 Planarity : 0.004 0.048 2394 Dihedral : 5.524 81.875 2386 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.79 % Allowed : 19.35 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1638 helix: 1.70 (0.23), residues: 530 sheet: -0.37 (0.30), residues: 306 loop : -0.43 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 190 TYR 0.015 0.001 TYR A 299 PHE 0.021 0.001 PHE A 337 TRP 0.025 0.001 TRP A 410 HIS 0.005 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00300 (13726) covalent geometry : angle 0.62365 (18619) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.48961 ( 8) hydrogen bonds : bond 0.03773 ( 508) hydrogen bonds : angle 4.73192 ( 1455) metal coordination : bond 0.00294 ( 4) link_ALPHA1-3 : bond 0.00675 ( 2) link_ALPHA1-3 : angle 1.49642 ( 6) link_ALPHA1-6 : bond 0.00364 ( 2) link_ALPHA1-6 : angle 1.53173 ( 6) link_BETA1-4 : bond 0.00340 ( 10) link_BETA1-4 : angle 1.58016 ( 30) link_NAG-ASN : bond 0.00290 ( 6) link_NAG-ASN : angle 1.27103 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8296 (mp0) cc_final: 0.8073 (mp0) REVERT: A 537 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 714 ASP cc_start: 0.7393 (t70) cc_final: 0.6788 (t70) REVERT: E 536 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7798 (ptp90) REVERT: E 537 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: E 560 GLU cc_start: 0.8221 (mp0) cc_final: 0.7623 (mp0) REVERT: E 714 ASP cc_start: 0.7041 (t70) cc_final: 0.6575 (t70) REVERT: H 44 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8716 (mp0) REVERT: H 79 MET cc_start: 0.7232 (mpt) cc_final: 0.6299 (mpt) REVERT: Q 5 GLN cc_start: 0.9265 (mp10) cc_final: 0.8979 (mp10) REVERT: Q 46 GLU cc_start: 0.8702 (tt0) cc_final: 0.8422 (pt0) outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 0.6244 time to fit residues: 104.2212 Evaluate side-chains 140 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 156 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 65 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.133080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106188 restraints weight = 89739.970| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 5.68 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13754 Z= 0.134 Angle : 0.633 10.980 18687 Z= 0.309 Chirality : 0.042 0.151 2019 Planarity : 0.004 0.048 2394 Dihedral : 5.571 81.867 2386 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.29 % Allowed : 20.07 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1638 helix: 1.70 (0.23), residues: 530 sheet: -0.16 (0.31), residues: 288 loop : -0.51 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 190 TYR 0.016 0.001 TYR E 299 PHE 0.018 0.001 PHE A 337 TRP 0.024 0.001 TRP A 410 HIS 0.005 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00320 (13726) covalent geometry : angle 0.62899 (18619) SS BOND : bond 0.00469 ( 4) SS BOND : angle 0.53633 ( 8) hydrogen bonds : bond 0.03905 ( 508) hydrogen bonds : angle 4.74898 ( 1455) metal coordination : bond 0.00341 ( 4) link_ALPHA1-3 : bond 0.00654 ( 2) link_ALPHA1-3 : angle 1.40897 ( 6) link_ALPHA1-6 : bond 0.00348 ( 2) link_ALPHA1-6 : angle 1.53208 ( 6) link_BETA1-4 : bond 0.00342 ( 10) link_BETA1-4 : angle 1.53834 ( 30) link_NAG-ASN : bond 0.00281 ( 6) link_NAG-ASN : angle 1.24213 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: A 714 ASP cc_start: 0.7452 (t70) cc_final: 0.6870 (t70) REVERT: E 536 ARG cc_start: 0.8177 (ptp90) cc_final: 0.7840 (ptp90) REVERT: E 537 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: E 560 GLU cc_start: 0.8244 (mp0) cc_final: 0.7661 (mp0) REVERT: E 714 ASP cc_start: 0.7186 (t70) cc_final: 0.6704 (t70) REVERT: H 44 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8716 (mp0) REVERT: H 79 MET cc_start: 0.7320 (mpt) cc_final: 0.6348 (mpt) REVERT: Q 5 GLN cc_start: 0.9323 (mp10) cc_final: 0.9085 (mp10) REVERT: Q 46 GLU cc_start: 0.8680 (tt0) cc_final: 0.8396 (pt0) outliers start: 15 outliers final: 11 residues processed: 145 average time/residue: 0.6268 time to fit residues: 100.2111 Evaluate side-chains 142 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 537 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 29 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 56 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 133 optimal weight: 0.0470 chunk 53 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.135281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108582 restraints weight = 84621.131| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 5.58 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13754 Z= 0.109 Angle : 0.627 12.923 18687 Z= 0.303 Chirality : 0.042 0.159 2019 Planarity : 0.004 0.050 2394 Dihedral : 5.487 82.039 2386 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.36 % Allowed : 20.22 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1638 helix: 1.79 (0.23), residues: 524 sheet: 0.16 (0.31), residues: 272 loop : -0.52 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 190 TYR 0.015 0.001 TYR E 299 PHE 0.019 0.001 PHE Q 68 TRP 0.025 0.001 TRP E 410 HIS 0.005 0.001 HIS E 697 Details of bonding type rmsd covalent geometry : bond 0.00255 (13726) covalent geometry : angle 0.62263 (18619) SS BOND : bond 0.00556 ( 4) SS BOND : angle 0.60663 ( 8) hydrogen bonds : bond 0.03474 ( 508) hydrogen bonds : angle 4.67232 ( 1455) metal coordination : bond 0.00123 ( 4) link_ALPHA1-3 : bond 0.00651 ( 2) link_ALPHA1-3 : angle 1.41177 ( 6) link_ALPHA1-6 : bond 0.00371 ( 2) link_ALPHA1-6 : angle 1.49664 ( 6) link_BETA1-4 : bond 0.00357 ( 10) link_BETA1-4 : angle 1.53060 ( 30) link_NAG-ASN : bond 0.00330 ( 6) link_NAG-ASN : angle 1.25140 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8322 (mp0) cc_final: 0.8100 (mp0) REVERT: A 537 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: A 648 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: A 714 ASP cc_start: 0.7457 (t70) cc_final: 0.6872 (t70) REVERT: E 536 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7766 (ptp90) REVERT: E 560 GLU cc_start: 0.8248 (mp0) cc_final: 0.7681 (mp0) REVERT: E 648 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: E 714 ASP cc_start: 0.7183 (t70) cc_final: 0.6678 (t70) REVERT: H 44 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8705 (mp0) REVERT: H 79 MET cc_start: 0.7239 (mpt) cc_final: 0.6312 (mpt) REVERT: Q 5 GLN cc_start: 0.9265 (mp10) cc_final: 0.9010 (mp10) REVERT: Q 46 GLU cc_start: 0.8725 (tt0) cc_final: 0.8359 (pt0) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.6216 time to fit residues: 100.4614 Evaluate side-chains 139 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 396 HIS Chi-restraints excluded: chain E residue 648 GLU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.129855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103294 restraints weight = 70520.292| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 5.10 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13754 Z= 0.220 Angle : 0.704 13.916 18687 Z= 0.346 Chirality : 0.045 0.165 2019 Planarity : 0.005 0.044 2394 Dihedral : 5.838 81.706 2386 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.51 % Allowed : 20.43 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1638 helix: 1.40 (0.23), residues: 530 sheet: -0.41 (0.30), residues: 296 loop : -0.55 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 190 TYR 0.019 0.002 TYR E 733 PHE 0.019 0.001 PHE A 337 TRP 0.039 0.002 TRP A 410 HIS 0.007 0.001 HIS E 618 Details of bonding type rmsd covalent geometry : bond 0.00526 (13726) covalent geometry : angle 0.70036 (18619) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.61575 ( 8) hydrogen bonds : bond 0.04944 ( 508) hydrogen bonds : angle 4.93205 ( 1455) metal coordination : bond 0.00736 ( 4) link_ALPHA1-3 : bond 0.00640 ( 2) link_ALPHA1-3 : angle 1.41419 ( 6) link_ALPHA1-6 : bond 0.00258 ( 2) link_ALPHA1-6 : angle 1.58714 ( 6) link_BETA1-4 : bond 0.00310 ( 10) link_BETA1-4 : angle 1.61768 ( 30) link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 1.30207 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.09 seconds wall clock time: 77 minutes 33.52 seconds (4653.52 seconds total)