Starting phenix.real_space_refine on Thu Feb 15 12:25:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytp_34091/02_2024/7ytp_34091_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 7782 2.51 5 N 2044 2.21 5 O 2298 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 605": "OD1" <-> "OD2" Residue "B TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12178 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5907 Classifications: {'peptide': 731} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 697} Chain breaks: 2 Chain: "B" Number of atoms: 5907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5907 Classifications: {'peptide': 731} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 697} Chain breaks: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'JRI': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'JRI': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.79, per 1000 atoms: 0.56 Number of scatterers: 12178 At special positions: 0 Unit cell: (100.845, 130.725, 99.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 F 2 9.00 O 2298 8.00 N 2044 7.00 C 7782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 787 " - pdb=" SG CYS A 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 36 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 263 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 787 " - pdb=" SG CYS B 814 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 66 " " NAG A1002 " - " ASN A 590 " " NAG A1003 " - " ASN A 413 " " NAG A1004 " - " ASN A 361 " " NAG A1005 " - " ASN A 679 " " NAG B1001 " - " ASN B 66 " " NAG B1002 " - " ASN B 590 " " NAG B1003 " - " ASN B 413 " " NAG B1004 " - " ASN B 361 " " NAG B1005 " - " ASN B 679 " " NAG C 1 " - " ASN A 215 " " NAG D 1 " - " ASN A 523 " " NAG E 1 " - " ASN A 69 " " NAG F 1 " - " ASN B 215 " " NAG G 1 " - " ASN B 523 " " NAG H 1 " - " ASN B 69 " Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 9 sheets defined 12.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.797A pdb=" N GLU A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.734A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 388 through 395 Proline residue: A 392 - end of helix removed outlier: 4.197A pdb=" N ASN A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 589 through 592 removed outlier: 4.406A pdb=" N THR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 592' Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.816A pdb=" N ARG A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 769 through 772 No H-bonds generated for 'chain 'A' and resid 769 through 772' Processing helix chain 'A' and resid 789 through 798 removed outlier: 3.848A pdb=" N VAL A 792 " --> pdb=" O CYS A 789 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TRP A 793 " --> pdb=" O ASP A 790 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 798 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'B' and resid 165 through 171 removed outlier: 4.662A pdb=" N GLU B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 307 through 310 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.728A pdb=" N GLY B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 388 through 395 Proline residue: B 392 - end of helix removed outlier: 4.166A pdb=" N ASN B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'B' and resid 589 through 592 removed outlier: 4.400A pdb=" N THR B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 589 through 592' Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 693 through 697 removed outlier: 3.766A pdb=" N ARG B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 721 No H-bonds generated for 'chain 'B' and resid 718 through 721' Processing helix chain 'B' and resid 769 through 774 removed outlier: 5.298A pdb=" N ASN B 774 " --> pdb=" O ASN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.839A pdb=" N VAL B 792 " --> pdb=" O CYS B 789 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TRP B 793 " --> pdb=" O ASP B 790 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.055A pdb=" N ASN A 69 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU A 93 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 131 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 152 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 176 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 208 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 229 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 253 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 294 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU A 318 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 344 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 374 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 401 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 425 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 497 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS A 521 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 546 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 570 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 600 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A 623 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A 654 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 530 through 532 removed outlier: 6.901A pdb=" N ARG A 553 " --> pdb=" O GLN A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 679 through 681 removed outlier: 5.889A pdb=" N THR A 703 " --> pdb=" O LEU A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 751 through 753 removed outlier: 6.163A pdb=" N MET A 777 " --> pdb=" O LEU A 752 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 37 through 41 removed outlier: 5.797A pdb=" N ASN B 69 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B 93 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 131 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 152 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 176 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 208 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 229 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 253 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 294 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 318 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN B 344 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 374 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.884A pdb=" N VAL B 425 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR B 497 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS B 521 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR B 546 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 570 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS B 600 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B 623 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU B 654 " --> pdb=" O LEU B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 530 through 532 removed outlier: 6.855A pdb=" N ARG B 553 " --> pdb=" O GLN B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 679 through 681 removed outlier: 5.693A pdb=" N THR B 703 " --> pdb=" O LEU B 680 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 751 through 753 removed outlier: 6.010A pdb=" N MET B 777 " --> pdb=" O LEU B 752 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 45 hydrogen bonds defined for protein. 45 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: 3.38 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1960 1.28 - 1.42: 2937 1.42 - 1.55: 7453 1.55 - 1.68: 2 1.68 - 1.82: 72 Bond restraints: 12424 Sorted by residual: bond pdb=" C1 NAG A1005 " pdb=" O5 NAG A1005 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" CB PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" CG PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 1.503 1.437 0.066 3.40e-02 8.65e+02 3.75e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 96.59 - 112.87: 7087 112.87 - 129.14: 9683 129.14 - 145.42: 66 145.42 - 161.69: 0 161.69 - 177.97: 2 Bond angle restraints: 16838 Sorted by residual: angle pdb=" N PRO B 148 " pdb=" CD PRO B 148 " pdb=" CG PRO B 148 " ideal model delta sigma weight residual 103.20 96.59 6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.81e+01 angle pdb=" N GLY A 686 " pdb=" CA GLY A 686 " pdb=" C GLY A 686 " ideal model delta sigma weight residual 116.01 109.88 6.13 1.64e+00 3.72e-01 1.40e+01 angle pdb=" C SER B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta sigma weight residual 121.97 128.07 -6.10 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA GLY A 686 " pdb=" C GLY A 686 " pdb=" N LEU A 687 " ideal model delta sigma weight residual 118.67 115.38 3.29 9.80e-01 1.04e+00 1.13e+01 ... (remaining 16833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7243 17.80 - 35.61: 534 35.61 - 53.41: 95 53.41 - 71.21: 34 71.21 - 89.02: 10 Dihedral angle restraints: 7916 sinusoidal: 3582 harmonic: 4334 Sorted by residual: dihedral pdb=" CB CYS B 263 " pdb=" SG CYS B 263 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual -86.00 -175.02 89.02 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 263 " pdb=" SG CYS A 263 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -173.93 87.93 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 521 " pdb=" CB CYS A 521 " ideal model delta sinusoidal sigma weight residual 93.00 37.04 55.96 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1717 0.060 - 0.120: 266 0.120 - 0.180: 24 0.180 - 0.240: 1 0.240 - 0.301: 2 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 66 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 66 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 69 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2007 not shown) Planarity restraints: 2122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 JRI B1006 " 0.130 2.00e-02 2.50e+03 1.08e-01 1.46e+02 pdb=" C5 JRI B1006 " 0.102 2.00e-02 2.50e+03 pdb=" C9 JRI B1006 " -0.048 2.00e-02 2.50e+03 pdb=" N2 JRI B1006 " -0.168 2.00e-02 2.50e+03 pdb=" O2 JRI B1006 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 JRI A1006 " -0.123 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" C5 JRI A1006 " -0.096 2.00e-02 2.50e+03 pdb=" C9 JRI A1006 " 0.046 2.00e-02 2.50e+03 pdb=" N2 JRI A1006 " 0.158 2.00e-02 2.50e+03 pdb=" O2 JRI A1006 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 147 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO B 148 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 148 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 148 " -0.059 5.00e-02 4.00e+02 ... (remaining 2119 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 434 2.72 - 3.27: 12284 3.27 - 3.81: 19560 3.81 - 4.36: 26584 4.36 - 4.90: 43084 Nonbonded interactions: 101946 Sorted by model distance: nonbonded pdb=" OE1 GLU A 93 " pdb=" OG SER A 131 " model vdw 2.179 2.440 nonbonded pdb=" O SER B 429 " pdb=" N ASN B 431 " model vdw 2.199 2.520 nonbonded pdb=" OG1 THR B 290 " pdb=" OE1 GLU B 291 " model vdw 2.223 2.440 nonbonded pdb=" O LEU A 223 " pdb=" ND2 ASN A 247 " model vdw 2.237 2.520 nonbonded pdb=" N LEU A 72 " pdb=" O ASP A 95 " model vdw 2.244 2.520 ... (remaining 101941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.620 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 34.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.003 0.119 12424 Z= 0.187 Angle : 0.598 7.776 16838 Z= 0.307 Chirality : 0.045 0.301 2010 Planarity : 0.005 0.110 2106 Dihedral : 13.078 87.343 5050 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.76 % Favored : 94.97 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1450 helix: -2.84 (0.40), residues: 126 sheet: -2.11 (0.35), residues: 282 loop : -0.35 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.004 0.000 HIS B 46 PHE 0.019 0.001 PHE A 690 TYR 0.012 0.001 TYR A 184 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.412 Fit side-chains REVERT: A 141 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6111 (mm-30) REVERT: A 395 ASN cc_start: 0.6825 (m-40) cc_final: 0.6395 (p0) REVERT: A 734 GLN cc_start: 0.6108 (tt0) cc_final: 0.5905 (mt0) REVERT: B 537 GLU cc_start: 0.7648 (mp0) cc_final: 0.7396 (mp0) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 1.1140 time to fit residues: 220.6288 Evaluate side-chains 133 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 9.9990 chunk 110 optimal weight: 0.0270 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 overall best weight: 2.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 187 ASN A 202 ASN A 534 ASN B 265 ASN B 337 HIS B 344 GLN B 354 GLN B 515 HIS B 534 ASN B 709 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12424 Z= 0.256 Angle : 0.642 9.316 16838 Z= 0.320 Chirality : 0.049 0.400 2010 Planarity : 0.004 0.069 2106 Dihedral : 6.888 59.320 2080 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.24 % Favored : 94.41 % Rotamer: Outliers : 1.38 % Allowed : 9.51 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.23), residues: 1450 helix: -3.12 (0.32), residues: 146 sheet: -2.18 (0.34), residues: 272 loop : -0.35 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 793 HIS 0.005 0.001 HIS A 337 PHE 0.025 0.002 PHE A 408 TYR 0.033 0.002 TYR B 356 ARG 0.011 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.407 Fit side-chains REVERT: A 151 GLN cc_start: 0.7379 (mt0) cc_final: 0.6970 (tt0) REVERT: A 164 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6248 (mtt180) REVERT: A 243 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6567 (p0) REVERT: A 395 ASN cc_start: 0.6944 (m-40) cc_final: 0.6499 (p0) REVERT: A 734 GLN cc_start: 0.6260 (tt0) cc_final: 0.6053 (mt0) REVERT: A 751 TYR cc_start: 0.7375 (t80) cc_final: 0.7037 (t80) REVERT: A 778 LEU cc_start: 0.6532 (tt) cc_final: 0.6254 (tp) REVERT: B 55 HIS cc_start: 0.6407 (m170) cc_final: 0.4394 (t-90) REVERT: B 370 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6956 (mtpp) REVERT: B 378 ARG cc_start: 0.7558 (mtp85) cc_final: 0.6974 (mtm110) REVERT: B 422 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.5909 (ptt180) REVERT: B 534 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6213 (t0) REVERT: B 537 GLU cc_start: 0.7971 (mp0) cc_final: 0.7668 (mp0) REVERT: B 752 LEU cc_start: 0.7986 (tp) cc_final: 0.7404 (mt) outliers start: 19 outliers final: 5 residues processed: 151 average time/residue: 1.1066 time to fit residues: 183.6206 Evaluate side-chains 132 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 534 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 187 ASN A 241 GLN A 534 ASN A 820 HIS B 55 HIS B 76 HIS B 276 ASN B 354 GLN B 708 HIS B 710 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 12424 Z= 0.425 Angle : 0.757 9.799 16838 Z= 0.376 Chirality : 0.054 0.349 2010 Planarity : 0.005 0.053 2106 Dihedral : 7.324 58.438 2080 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 3.05 % Allowed : 11.76 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1450 helix: -3.36 (0.29), residues: 164 sheet: -2.33 (0.33), residues: 272 loop : -0.39 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 309 HIS 0.007 0.002 HIS B 708 PHE 0.024 0.003 PHE A 408 TYR 0.042 0.003 TYR B 356 ARG 0.006 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.6839 (mtm-85) cc_final: 0.6526 (mtt180) REVERT: A 167 GLN cc_start: 0.6473 (OUTLIER) cc_final: 0.6163 (mm110) REVERT: A 243 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 395 ASN cc_start: 0.7175 (m-40) cc_final: 0.6676 (p0) REVERT: A 778 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6358 (tp) REVERT: B 96 PHE cc_start: 0.6995 (t80) cc_final: 0.6725 (t80) REVERT: B 169 THR cc_start: 0.7207 (m) cc_final: 0.6890 (p) REVERT: B 275 ASN cc_start: 0.7396 (m-40) cc_final: 0.7185 (m110) REVERT: B 378 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7031 (mtm180) REVERT: B 422 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.6059 (ptt180) REVERT: B 537 GLU cc_start: 0.8043 (mp0) cc_final: 0.7746 (mp0) REVERT: B 603 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: B 616 MET cc_start: 0.8570 (mtp) cc_final: 0.8200 (mtp) REVERT: B 699 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7726 (mttm) REVERT: B 710 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.6108 (mm110) REVERT: B 782 HIS cc_start: 0.5428 (m90) cc_final: 0.5200 (m90) outliers start: 42 outliers final: 10 residues processed: 160 average time/residue: 1.1960 time to fit residues: 209.8206 Evaluate side-chains 132 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 699 LYS Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 534 ASN ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 167 GLN B 246 ASN B 276 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 820 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 12424 Z= 0.496 Angle : 0.804 10.322 16838 Z= 0.399 Chirality : 0.055 0.301 2010 Planarity : 0.006 0.053 2106 Dihedral : 7.579 56.355 2080 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.97 % Favored : 92.76 % Rotamer: Outliers : 3.48 % Allowed : 13.50 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.22), residues: 1450 helix: -3.59 (0.29), residues: 152 sheet: -2.53 (0.34), residues: 240 loop : -0.64 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 309 HIS 0.022 0.002 HIS A 820 PHE 0.025 0.003 PHE B 690 TYR 0.026 0.003 TYR B 356 ARG 0.008 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6597 (mtm110) REVERT: A 243 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6720 (p0) REVERT: A 275 ASN cc_start: 0.7338 (m-40) cc_final: 0.7009 (m-40) REVERT: A 377 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7795 (mt) REVERT: A 676 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7738 (t0) REVERT: A 734 GLN cc_start: 0.6938 (tt0) cc_final: 0.6705 (tm-30) REVERT: A 778 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6431 (tt) REVERT: B 94 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6712 (mt) REVERT: B 169 THR cc_start: 0.7320 (m) cc_final: 0.6904 (p) REVERT: B 223 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 275 ASN cc_start: 0.7478 (m-40) cc_final: 0.7203 (m-40) REVERT: B 422 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.6016 (ptt180) REVERT: B 603 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: B 676 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7371 (t0) REVERT: B 777 MET cc_start: 0.6574 (mmm) cc_final: 0.6143 (tpt) outliers start: 48 outliers final: 14 residues processed: 162 average time/residue: 1.0485 time to fit residues: 187.6517 Evaluate side-chains 145 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 126 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 246 ASN A 534 ASN A 820 HIS B 265 ASN B 276 ASN B 280 GLN B 534 ASN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12424 Z= 0.155 Angle : 0.572 9.542 16838 Z= 0.285 Chirality : 0.047 0.377 2010 Planarity : 0.004 0.050 2106 Dihedral : 6.579 56.627 2080 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.24 % Favored : 94.48 % Rotamer: Outliers : 2.18 % Allowed : 15.75 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1450 helix: -3.43 (0.31), residues: 142 sheet: -2.30 (0.33), residues: 272 loop : -0.44 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 797 HIS 0.007 0.001 HIS A 820 PHE 0.022 0.001 PHE B 690 TYR 0.015 0.002 TYR A 380 ARG 0.004 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: A 243 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6693 (p0) REVERT: A 275 ASN cc_start: 0.7467 (m-40) cc_final: 0.7124 (m-40) REVERT: B 169 THR cc_start: 0.7268 (m) cc_final: 0.6856 (p) REVERT: B 175 GLU cc_start: 0.7739 (tp30) cc_final: 0.7508 (mm-30) REVERT: B 275 ASN cc_start: 0.7498 (m-40) cc_final: 0.7203 (m-40) REVERT: B 378 ARG cc_start: 0.7523 (mtp85) cc_final: 0.6642 (mtp180) REVERT: B 422 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6089 (ptt180) REVERT: B 777 MET cc_start: 0.6276 (mmm) cc_final: 0.5836 (tpt) outliers start: 30 outliers final: 8 residues processed: 154 average time/residue: 0.9788 time to fit residues: 167.9335 Evaluate side-chains 136 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 778 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 202 ASN A 800 HIS A 820 HIS B 55 HIS B 276 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.078 12424 Z= 0.699 Angle : 0.933 11.062 16838 Z= 0.459 Chirality : 0.061 0.300 2010 Planarity : 0.007 0.065 2106 Dihedral : 8.005 59.928 2080 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.00 % Favored : 91.59 % Rotamer: Outliers : 3.77 % Allowed : 16.04 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1450 helix: -3.70 (0.29), residues: 112 sheet: -2.56 (0.31), residues: 260 loop : -0.67 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 797 HIS 0.023 0.002 HIS A 820 PHE 0.030 0.004 PHE A 506 TYR 0.021 0.004 TYR A 233 ARG 0.010 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: A 195 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 243 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6750 (p0) REVERT: A 275 ASN cc_start: 0.7559 (m-40) cc_final: 0.7196 (m-40) REVERT: A 377 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 383 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8563 (tttm) REVERT: A 710 GLN cc_start: 0.7631 (tt0) cc_final: 0.7428 (tt0) REVERT: A 778 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6478 (tt) REVERT: B 151 GLN cc_start: 0.6927 (mt0) cc_final: 0.6296 (mt0) REVERT: B 169 THR cc_start: 0.7509 (m) cc_final: 0.7030 (p) REVERT: B 197 LYS cc_start: 0.7234 (tptt) cc_final: 0.6949 (tppt) REVERT: B 243 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: B 275 ASN cc_start: 0.7745 (m-40) cc_final: 0.7427 (m110) REVERT: B 422 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6050 (ptt180) REVERT: B 688 LYS cc_start: 0.6493 (mmtt) cc_final: 0.6041 (tttt) REVERT: B 777 MET cc_start: 0.6657 (mmm) cc_final: 0.6334 (tpt) REVERT: B 782 HIS cc_start: 0.5364 (m90) cc_final: 0.4512 (m-70) outliers start: 52 outliers final: 26 residues processed: 157 average time/residue: 1.0479 time to fit residues: 182.2690 Evaluate side-chains 150 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 116 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 767 PHE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 820 HIS B 55 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12424 Z= 0.206 Angle : 0.619 9.610 16838 Z= 0.312 Chirality : 0.050 0.530 2010 Planarity : 0.004 0.050 2106 Dihedral : 7.004 58.850 2080 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.79 % Rotamer: Outliers : 3.05 % Allowed : 17.34 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.22), residues: 1450 helix: -3.39 (0.32), residues: 112 sheet: -2.35 (0.32), residues: 268 loop : -0.58 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 797 HIS 0.015 0.001 HIS A 820 PHE 0.024 0.002 PHE A 690 TYR 0.018 0.002 TYR A 185 ARG 0.002 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6709 (p0) REVERT: A 275 ASN cc_start: 0.7481 (m-40) cc_final: 0.7175 (m-40) REVERT: A 383 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8424 (tttm) REVERT: A 710 GLN cc_start: 0.7365 (tt0) cc_final: 0.7044 (tt0) REVERT: A 778 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6491 (tt) REVERT: B 151 GLN cc_start: 0.6915 (mt0) cc_final: 0.6211 (mt0) REVERT: B 169 THR cc_start: 0.7467 (m) cc_final: 0.7041 (p) REVERT: B 197 LYS cc_start: 0.7084 (tptt) cc_final: 0.6842 (tppt) REVERT: B 243 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: B 275 ASN cc_start: 0.7650 (m-40) cc_final: 0.7317 (m-40) REVERT: B 378 ARG cc_start: 0.7557 (mtp85) cc_final: 0.6652 (mtp180) REVERT: B 422 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6092 (ptt180) REVERT: B 734 GLN cc_start: 0.6508 (mt0) cc_final: 0.5908 (mp-120) REVERT: B 777 MET cc_start: 0.6366 (mmm) cc_final: 0.6045 (tpt) outliers start: 42 outliers final: 24 residues processed: 154 average time/residue: 1.0010 time to fit residues: 171.2061 Evaluate side-chains 149 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 820 HIS A 823 GLN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12424 Z= 0.328 Angle : 0.677 9.840 16838 Z= 0.337 Chirality : 0.051 0.432 2010 Planarity : 0.005 0.050 2106 Dihedral : 7.196 59.859 2080 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.10 % Favored : 92.62 % Rotamer: Outliers : 3.34 % Allowed : 17.85 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1450 helix: -3.37 (0.32), residues: 112 sheet: -2.33 (0.32), residues: 268 loop : -0.56 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 797 HIS 0.016 0.001 HIS A 820 PHE 0.021 0.002 PHE B 690 TYR 0.017 0.002 TYR A 185 ARG 0.004 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7312 (mt-10) REVERT: A 243 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6717 (p0) REVERT: A 275 ASN cc_start: 0.7518 (m-40) cc_final: 0.7209 (m110) REVERT: A 377 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 383 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8448 (tttm) REVERT: A 778 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6609 (tt) REVERT: B 151 GLN cc_start: 0.6835 (mt0) cc_final: 0.6130 (mt0) REVERT: B 169 THR cc_start: 0.7474 (m) cc_final: 0.7066 (p) REVERT: B 197 LYS cc_start: 0.7120 (tptt) cc_final: 0.6842 (tppt) REVERT: B 243 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6517 (m-30) REVERT: B 275 ASN cc_start: 0.7619 (m-40) cc_final: 0.7270 (m110) REVERT: B 377 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 422 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.6062 (ptt180) REVERT: B 551 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: B 710 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: B 734 GLN cc_start: 0.6607 (mt0) cc_final: 0.5969 (mp-120) REVERT: B 777 MET cc_start: 0.6581 (mmm) cc_final: 0.6194 (tpt) REVERT: B 782 HIS cc_start: 0.5351 (m90) cc_final: 0.4239 (m-70) outliers start: 46 outliers final: 23 residues processed: 157 average time/residue: 0.9606 time to fit residues: 168.1277 Evaluate side-chains 155 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 710 GLN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 820 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 12424 Z= 0.441 Angle : 0.754 10.082 16838 Z= 0.374 Chirality : 0.054 0.389 2010 Planarity : 0.005 0.050 2106 Dihedral : 7.506 58.593 2080 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.45 % Favored : 92.28 % Rotamer: Outliers : 3.19 % Allowed : 18.43 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1450 helix: -3.46 (0.30), residues: 124 sheet: -2.56 (0.33), residues: 240 loop : -0.67 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 797 HIS 0.016 0.002 HIS A 820 PHE 0.030 0.003 PHE A 690 TYR 0.028 0.003 TYR A 185 ARG 0.006 0.001 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6735 (p0) REVERT: A 275 ASN cc_start: 0.7481 (m-40) cc_final: 0.7159 (m110) REVERT: A 377 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7665 (mt) REVERT: A 383 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8489 (tttm) REVERT: A 778 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6543 (tt) REVERT: B 151 GLN cc_start: 0.6872 (mt0) cc_final: 0.6263 (mt0) REVERT: B 169 THR cc_start: 0.7494 (m) cc_final: 0.7091 (p) REVERT: B 197 LYS cc_start: 0.7174 (tptt) cc_final: 0.6832 (tppp) REVERT: B 243 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: B 275 ASN cc_start: 0.7663 (m-40) cc_final: 0.7321 (m110) REVERT: B 377 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 422 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6104 (ptt180) REVERT: B 551 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7950 (m-40) REVERT: B 734 GLN cc_start: 0.6656 (mt0) cc_final: 0.6050 (mp-120) REVERT: B 777 MET cc_start: 0.6661 (mmm) cc_final: 0.6312 (tpt) REVERT: B 782 HIS cc_start: 0.5413 (m90) cc_final: 0.4320 (m-70) outliers start: 44 outliers final: 26 residues processed: 158 average time/residue: 0.9923 time to fit residues: 174.5915 Evaluate side-chains 157 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 145 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 820 HIS ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12424 Z= 0.142 Angle : 0.575 9.564 16838 Z= 0.289 Chirality : 0.047 0.403 2010 Planarity : 0.004 0.050 2106 Dihedral : 6.655 56.980 2080 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.38 % Favored : 94.34 % Rotamer: Outliers : 2.25 % Allowed : 19.38 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1450 helix: -2.82 (0.37), residues: 112 sheet: -1.81 (0.36), residues: 232 loop : -0.63 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 635 HIS 0.027 0.001 HIS A 820 PHE 0.029 0.001 PHE A 690 TYR 0.022 0.001 TYR A 185 ARG 0.002 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2900 Ramachandran restraints generated. 1450 Oldfield, 0 Emsley, 1450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6710 (p0) REVERT: A 275 ASN cc_start: 0.7458 (m-40) cc_final: 0.7124 (m110) REVERT: A 383 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8359 (tttm) REVERT: B 151 GLN cc_start: 0.6876 (mt0) cc_final: 0.6153 (mt0) REVERT: B 169 THR cc_start: 0.7449 (m) cc_final: 0.7064 (p) REVERT: B 197 LYS cc_start: 0.7024 (tptt) cc_final: 0.6782 (tppt) REVERT: B 243 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6488 (m-30) REVERT: B 275 ASN cc_start: 0.7592 (m-40) cc_final: 0.7245 (m110) REVERT: B 377 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8487 (mm) REVERT: B 422 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6094 (ptt180) REVERT: B 734 GLN cc_start: 0.6544 (mt0) cc_final: 0.5885 (mp-120) REVERT: B 777 MET cc_start: 0.6273 (mmm) cc_final: 0.5959 (tpt) outliers start: 31 outliers final: 18 residues processed: 147 average time/residue: 1.0120 time to fit residues: 165.2546 Evaluate side-chains 146 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 820 HIS Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 ARG Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 812 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 734 GLN A 820 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.190003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126693 restraints weight = 12565.655| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.66 r_work: 0.3166 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12424 Z= 0.276 Angle : 0.640 9.732 16838 Z= 0.319 Chirality : 0.050 0.338 2010 Planarity : 0.004 0.049 2106 Dihedral : 6.807 59.004 2080 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.28 % Favored : 93.45 % Rotamer: Outliers : 2.18 % Allowed : 19.67 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.22), residues: 1450 helix: -2.87 (0.36), residues: 112 sheet: -1.78 (0.35), residues: 242 loop : -0.63 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 797 HIS 0.015 0.001 HIS A 820 PHE 0.029 0.002 PHE A 690 TYR 0.014 0.002 TYR A 233 ARG 0.004 0.001 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.58 seconds wall clock time: 71 minutes 36.73 seconds (4296.73 seconds total)