Starting phenix.real_space_refine on Fri Feb 16 21:20:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/02_2024/6xnx_22272.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Zn 2 6.06 5 P 110 5.49 5 Mg 4 5.21 5 S 106 5.16 5 C 10116 2.51 5 N 2888 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 834": "OD1" <-> "OD2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "C TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 536": "OD1" <-> "OD2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C ASP 573": "OD1" <-> "OD2" Residue "C PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 774": "OD1" <-> "OD2" Residue "C TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ASP 864": "OD1" <-> "OD2" Residue "C PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 948": "OE1" <-> "OE2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D ASP 310": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16540 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4407 Classifications: {'peptide': 549} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "B" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2678 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "C" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4401 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2688 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Chain: "x" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 644 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "y" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 564 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "I" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2078 SG CYS A 727 67.283 86.310 61.612 1.00 41.02 S ATOM 2099 SG CYS A 730 67.279 89.825 63.913 1.00 40.07 S ATOM 9163 SG CYS C 727 66.679 22.583 62.396 1.00 40.59 S ATOM 9184 SG CYS C 730 66.702 19.139 64.824 1.00 40.18 S Time building chain proxies: 9.03, per 1000 atoms: 0.55 Number of scatterers: 16540 At special positions: 0 Unit cell: (134.4, 109.2, 113.4, 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 2 29.99 S 106 16.00 P 110 15.00 Mg 4 11.99 O 3314 8.00 N 2888 7.00 C 10116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 8.44 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 35.9% alpha, 22.3% beta 54 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.903A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 824 through 840 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.675A pdb=" N GLU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 957 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.645A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.606A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.803A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 492 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.689A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 581 removed outlier: 4.873A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 684 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 975 Processing helix chain 'C' and resid 979 through 995 removed outlier: 4.805A pdb=" N MET C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.719A pdb=" N PHE B 24 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.150A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.014A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AB1, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.431A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.795A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.160A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS D 127 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR D 108 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.351A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.791A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.882A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 279 682 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4859 1.33 - 1.45: 3758 1.45 - 1.57: 8146 1.57 - 1.69: 217 1.69 - 1.81: 164 Bond restraints: 17144 Sorted by residual: bond pdb=" CA LEU C 657 " pdb=" CB LEU C 657 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.39e-02 5.18e+03 2.52e+01 bond pdb=" O3' DA y 30 " pdb=" P DC y 31 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.16e-02 7.43e+03 1.14e+01 bond pdb=" CA ALA B 211 " pdb=" CB ALA B 211 " ideal model delta sigma weight residual 1.525 1.484 0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" O3' DC x 57 " pdb=" P DC x 58 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.73e+00 ... (remaining 17139 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.66: 692 104.66 - 112.24: 8817 112.24 - 119.82: 6047 119.82 - 127.40: 7728 127.40 - 134.98: 369 Bond angle restraints: 23653 Sorted by residual: angle pdb=" C ASP A 834 " pdb=" CA ASP A 834 " pdb=" CB ASP A 834 " ideal model delta sigma weight residual 110.96 101.35 9.61 1.54e+00 4.22e-01 3.89e+01 angle pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " ideal model delta sigma weight residual 112.00 99.28 12.72 2.20e+00 2.07e-01 3.34e+01 angle pdb=" CA ASP A 792 " pdb=" C ASP A 792 " pdb=" O ASP A 792 " ideal model delta sigma weight residual 121.66 116.48 5.18 1.17e+00 7.31e-01 1.96e+01 angle pdb=" C4' DG y 35 " pdb=" O4' DG y 35 " pdb=" C1' DG y 35 " ideal model delta sigma weight residual 109.70 103.10 6.60 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C4' DG x 46 " pdb=" O4' DG x 46 " pdb=" C1' DG x 46 " ideal model delta sigma weight residual 109.70 103.26 6.44 1.50e+00 4.44e-01 1.84e+01 ... (remaining 23648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 9269 33.58 - 67.15: 704 67.15 - 100.73: 18 100.73 - 134.30: 0 134.30 - 167.88: 3 Dihedral angle restraints: 9994 sinusoidal: 4816 harmonic: 5178 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA TYR A 725 " pdb=" C TYR A 725 " pdb=" N ILE A 726 " pdb=" CA ILE A 726 " ideal model delta harmonic sigma weight residual -180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA TYR C 725 " pdb=" C TYR C 725 " pdb=" N ILE C 726 " pdb=" CA ILE C 726 " ideal model delta harmonic sigma weight residual 180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 9991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2117 0.077 - 0.155: 435 0.155 - 0.232: 25 0.232 - 0.310: 1 0.310 - 0.387: 6 Chirality restraints: 2584 Sorted by residual: chirality pdb=" CA TRP B 317 " pdb=" N TRP B 317 " pdb=" C TRP B 317 " pdb=" CB TRP B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASP A 792 " pdb=" N ASP A 792 " pdb=" C ASP A 792 " pdb=" CB ASP A 792 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASP A 834 " pdb=" N ASP A 834 " pdb=" C ASP A 834 " pdb=" CB ASP A 834 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2581 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 233 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU D 233 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU D 233 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR D 234 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT x 43 " 0.043 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" N1 DT x 43 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT x 43 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT x 43 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DT x 43 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT x 43 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT x 43 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT x 43 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT x 43 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT x 43 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y 30 " 0.039 2.00e-02 2.50e+03 1.87e-02 9.64e+00 pdb=" N9 DA y 30 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DA y 30 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA y 30 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA y 30 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DA y 30 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA y 30 " 0.023 2.00e-02 2.50e+03 pdb=" N1 DA y 30 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA y 30 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA y 30 " -0.007 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 94 2.36 - 2.99: 9762 2.99 - 3.63: 29509 3.63 - 4.26: 48409 4.26 - 4.90: 74533 Nonbonded interactions: 162307 Sorted by model distance: nonbonded pdb=" O GLY A 601 " pdb="MG MG A1101 " model vdw 1.724 2.170 nonbonded pdb=" OP2 DC y 36 " pdb="MG MG A1101 " model vdw 1.901 2.170 nonbonded pdb=" O GLY C 601 " pdb="MG MG x 101 " model vdw 1.937 2.170 nonbonded pdb=" OE2 GLU A 662 " pdb="MG MG A1102 " model vdw 1.999 2.170 nonbonded pdb=" O ASN D 117 " pdb=" OD1 ASN D 117 " model vdw 2.015 3.040 ... (remaining 162302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 460 through 1007 or resid 1102 through 1103)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 335 or resid 339 through 350)) selection = (chain 'D' and (resid 1 through 335 or resid 339 through 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.090 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 59.070 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.013 0.089 17144 Z= 0.826 Angle : 0.790 12.718 23653 Z= 0.464 Chirality : 0.060 0.387 2584 Planarity : 0.004 0.039 2643 Dihedral : 20.133 167.880 6658 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 2.35 % Allowed : 11.90 % Favored : 85.75 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.16), residues: 1766 helix: -2.27 (0.17), residues: 565 sheet: -3.52 (0.24), residues: 284 loop : -2.93 (0.17), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 317 HIS 0.008 0.001 HIS B 181 PHE 0.017 0.002 PHE D 206 TYR 0.015 0.002 TYR A 928 ARG 0.006 0.001 ARG A 773 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 296 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7846 (m-80) cc_final: 0.7334 (m-80) REVERT: A 827 LYS cc_start: 0.8199 (tptm) cc_final: 0.7996 (tttp) REVERT: A 861 GLU cc_start: 0.6737 (tt0) cc_final: 0.6514 (mm-30) REVERT: A 949 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7865 (ttp-170) REVERT: B 322 MET cc_start: 0.7600 (mtp) cc_final: 0.7343 (mtm) REVERT: C 571 GLU cc_start: 0.7697 (tt0) cc_final: 0.7441 (tt0) REVERT: C 627 MET cc_start: 0.9039 (mmm) cc_final: 0.8667 (mmm) REVERT: C 659 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 691 MET cc_start: 0.8335 (mtp) cc_final: 0.7882 (mtm) REVERT: C 780 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7986 (t) REVERT: C 848 MET cc_start: 0.7428 (ttp) cc_final: 0.7212 (ttp) REVERT: D 237 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7105 (ttm-80) REVERT: D 269 ASP cc_start: 0.7103 (m-30) cc_final: 0.6812 (m-30) REVERT: D 316 ILE cc_start: 0.8332 (mp) cc_final: 0.8100 (mt) outliers start: 37 outliers final: 19 residues processed: 330 average time/residue: 1.3570 time to fit residues: 495.8837 Evaluate side-chains 208 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS A 744 HIS A 763 ASN B 23 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 54 HIS B 101 ASN B 166 GLN B 227 ASN B 278 GLN B 282 GLN C1006 HIS D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17144 Z= 0.290 Angle : 0.662 11.340 23653 Z= 0.360 Chirality : 0.044 0.161 2584 Planarity : 0.005 0.036 2643 Dihedral : 22.292 178.908 3191 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 4.39 % Allowed : 17.43 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.18), residues: 1766 helix: -0.68 (0.20), residues: 571 sheet: -3.00 (0.24), residues: 303 loop : -1.98 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 317 HIS 0.013 0.002 HIS C 942 PHE 0.017 0.002 PHE D 29 TYR 0.023 0.002 TYR A 707 ARG 0.008 0.001 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 235 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7798 (m-80) cc_final: 0.7226 (m-80) REVERT: A 818 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6205 (m-70) REVERT: A 861 GLU cc_start: 0.6778 (tt0) cc_final: 0.6425 (mm-30) REVERT: B 49 ASP cc_start: 0.7743 (m-30) cc_final: 0.7478 (m-30) REVERT: B 334 ASP cc_start: 0.5181 (t70) cc_final: 0.4746 (t0) REVERT: C 627 MET cc_start: 0.8810 (mmm) cc_final: 0.8596 (mmm) REVERT: C 659 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8567 (mt) REVERT: C 691 MET cc_start: 0.8362 (mtp) cc_final: 0.7902 (mtm) REVERT: C 797 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: D 179 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (mt) REVERT: D 316 ILE cc_start: 0.8293 (mp) cc_final: 0.8026 (mt) outliers start: 69 outliers final: 19 residues processed: 281 average time/residue: 1.1394 time to fit residues: 361.2734 Evaluate side-chains 211 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 915 ARG Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 166 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS A 763 ASN B 227 ASN B 278 GLN C 744 HIS C 818 HIS C1006 HIS D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 0.057 17144 Z= 0.260 Angle : 0.622 10.573 23653 Z= 0.338 Chirality : 0.043 0.196 2584 Planarity : 0.004 0.040 2643 Dihedral : 22.176 177.283 3175 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 4.58 % Allowed : 20.36 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1766 helix: -0.02 (0.20), residues: 582 sheet: -2.72 (0.24), residues: 340 loop : -1.53 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 307 HIS 0.008 0.001 HIS C 942 PHE 0.013 0.002 PHE D 29 TYR 0.019 0.002 TYR C 725 ARG 0.009 0.001 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 223 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7741 (m-80) cc_final: 0.7254 (m-80) REVERT: A 818 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6189 (m-70) REVERT: A 861 GLU cc_start: 0.6776 (tt0) cc_final: 0.6432 (mm-30) REVERT: B 49 ASP cc_start: 0.7674 (m-30) cc_final: 0.7412 (m-30) REVERT: B 77 THR cc_start: 0.8145 (t) cc_final: 0.7864 (p) REVERT: B 219 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 228 ILE cc_start: 0.8382 (pp) cc_final: 0.8120 (pp) REVERT: C 627 MET cc_start: 0.8734 (mmm) cc_final: 0.8511 (mmm) REVERT: C 691 MET cc_start: 0.8368 (mtp) cc_final: 0.7812 (mtm) REVERT: C 797 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: D 179 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8259 (mt) outliers start: 72 outliers final: 20 residues processed: 270 average time/residue: 1.0807 time to fit residues: 331.9600 Evaluate side-chains 223 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 0.1980 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS A 740 ASN C 818 HIS C1004 ASN D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17144 Z= 0.228 Angle : 0.605 8.501 23653 Z= 0.328 Chirality : 0.042 0.150 2584 Planarity : 0.004 0.068 2643 Dihedral : 22.086 178.636 3171 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 4.77 % Allowed : 21.12 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1766 helix: 0.27 (0.21), residues: 584 sheet: -2.54 (0.23), residues: 361 loop : -1.22 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 307 HIS 0.019 0.001 HIS C 818 PHE 0.013 0.002 PHE D 29 TYR 0.027 0.002 TYR A 725 ARG 0.008 0.001 ARG C 855 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 218 time to evaluate : 1.904 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7755 (m-80) cc_final: 0.7414 (m-80) REVERT: C 627 MET cc_start: 0.8661 (mmm) cc_final: 0.8451 (mmm) REVERT: C 659 LEU cc_start: 0.8932 (mt) cc_final: 0.8616 (mt) REVERT: C 691 MET cc_start: 0.8359 (mtp) cc_final: 0.7833 (mtm) REVERT: C 797 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: C 839 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7971 (mtmt) REVERT: D 5 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7720 (ttt) REVERT: D 179 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8216 (mt) outliers start: 75 outliers final: 26 residues processed: 261 average time/residue: 1.1715 time to fit residues: 344.8301 Evaluate side-chains 224 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN A 763 ASN A 990 HIS C 482 HIS D 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17144 Z= 0.376 Angle : 0.660 11.020 23653 Z= 0.354 Chirality : 0.044 0.169 2584 Planarity : 0.004 0.035 2643 Dihedral : 22.214 177.447 3170 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 4.90 % Allowed : 22.14 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1766 helix: 0.25 (0.21), residues: 582 sheet: -2.43 (0.25), residues: 342 loop : -1.07 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 317 HIS 0.037 0.002 HIS C 818 PHE 0.019 0.002 PHE B 24 TYR 0.022 0.002 TYR C 725 ARG 0.009 0.001 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 206 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7405 (t0) cc_final: 0.7129 (t0) REVERT: A 584 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7186 (p0) REVERT: A 731 ASP cc_start: 0.7648 (p0) cc_final: 0.7145 (p0) REVERT: A 743 PHE cc_start: 0.7825 (m-80) cc_final: 0.7466 (m-80) REVERT: A 923 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7440 (mtpp) REVERT: C 659 LEU cc_start: 0.8979 (mt) cc_final: 0.8742 (mt) REVERT: C 691 MET cc_start: 0.8487 (mtp) cc_final: 0.7961 (mtm) REVERT: C 797 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: D 5 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7620 (ttt) REVERT: D 179 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8423 (mt) REVERT: D 262 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8403 (mp) outliers start: 77 outliers final: 32 residues processed: 254 average time/residue: 1.0965 time to fit residues: 315.5644 Evaluate side-chains 223 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN D 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17144 Z= 0.472 Angle : 0.705 10.831 23653 Z= 0.375 Chirality : 0.046 0.188 2584 Planarity : 0.005 0.041 2643 Dihedral : 22.331 177.817 3170 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 5.34 % Allowed : 23.09 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.19), residues: 1766 helix: 0.14 (0.20), residues: 584 sheet: -2.45 (0.26), residues: 316 loop : -1.12 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 317 HIS 0.008 0.002 HIS C 836 PHE 0.016 0.002 PHE B 48 TYR 0.028 0.002 TYR A 725 ARG 0.010 0.001 ARG A 855 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 200 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7463 (t0) cc_final: 0.7228 (t0) REVERT: A 584 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7288 (p0) REVERT: A 731 ASP cc_start: 0.7753 (p0) cc_final: 0.7328 (p0) REVERT: A 743 PHE cc_start: 0.7839 (m-80) cc_final: 0.7445 (m-80) REVERT: B 52 GLN cc_start: 0.7339 (mm110) cc_final: 0.7069 (pp30) REVERT: C 627 MET cc_start: 0.8680 (mmm) cc_final: 0.8475 (mmm) REVERT: C 659 LEU cc_start: 0.9009 (mt) cc_final: 0.8783 (mt) REVERT: C 797 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: C 824 GLU cc_start: 0.7281 (pp20) cc_final: 0.7076 (pp20) REVERT: C 827 LYS cc_start: 0.8327 (tttt) cc_final: 0.7917 (tttm) REVERT: C 896 SER cc_start: 0.8211 (m) cc_final: 0.7979 (m) REVERT: D 5 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7623 (ttt) outliers start: 84 outliers final: 42 residues processed: 254 average time/residue: 1.0994 time to fit residues: 316.2753 Evaluate side-chains 246 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 227 ASN D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17144 Z= 0.290 Angle : 0.644 11.088 23653 Z= 0.343 Chirality : 0.043 0.163 2584 Planarity : 0.004 0.036 2643 Dihedral : 22.226 179.795 3170 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 5.34 % Allowed : 23.47 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1766 helix: 0.32 (0.21), residues: 583 sheet: -2.36 (0.26), residues: 318 loop : -0.98 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 307 HIS 0.005 0.001 HIS D 222 PHE 0.014 0.002 PHE A 911 TYR 0.026 0.002 TYR A 725 ARG 0.009 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 230 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7344 (t0) cc_final: 0.7137 (t0) REVERT: A 584 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7214 (p0) REVERT: A 731 ASP cc_start: 0.7501 (p0) cc_final: 0.7102 (p0) REVERT: A 743 PHE cc_start: 0.7791 (m-80) cc_final: 0.7414 (m-80) REVERT: A 828 ARG cc_start: 0.7432 (tpp80) cc_final: 0.7116 (ttm-80) REVERT: B 322 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7087 (mtm) REVERT: C 797 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: C 827 LYS cc_start: 0.8308 (tttt) cc_final: 0.7955 (tttm) REVERT: D 5 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7141 (tpt) REVERT: D 143 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: D 148 ARG cc_start: 0.7649 (mmm-85) cc_final: 0.7365 (mmt90) REVERT: D 278 GLN cc_start: 0.8366 (mt0) cc_final: 0.8059 (mt0) REVERT: D 282 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6544 (tm-30) outliers start: 84 outliers final: 38 residues processed: 284 average time/residue: 1.0200 time to fit residues: 331.4259 Evaluate side-chains 248 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 267 ASN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN A 830 GLN B 23 ASN B 227 ASN C 818 HIS D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17144 Z= 0.246 Angle : 0.636 14.209 23653 Z= 0.337 Chirality : 0.042 0.196 2584 Planarity : 0.004 0.036 2643 Dihedral : 22.134 179.928 3170 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 4.52 % Allowed : 24.75 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1766 helix: 0.43 (0.21), residues: 582 sheet: -2.32 (0.27), residues: 299 loop : -0.96 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 307 HIS 0.006 0.001 HIS C 818 PHE 0.032 0.002 PHE A 475 TYR 0.025 0.002 TYR A 725 ARG 0.008 0.001 ARG C 855 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7306 (t0) cc_final: 0.7073 (t0) REVERT: A 584 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7122 (p0) REVERT: A 731 ASP cc_start: 0.7424 (p0) cc_final: 0.6998 (p0) REVERT: A 743 PHE cc_start: 0.7723 (m-80) cc_final: 0.7469 (m-10) REVERT: A 877 GLU cc_start: 0.7372 (tp30) cc_final: 0.7086 (tp30) REVERT: B 219 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 233 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 797 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: C 827 LYS cc_start: 0.8271 (tttt) cc_final: 0.7947 (tttm) REVERT: D 5 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7139 (tpt) REVERT: D 148 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7401 (mmt90) REVERT: D 298 GLU cc_start: 0.6995 (mp0) cc_final: 0.6767 (mp0) outliers start: 71 outliers final: 34 residues processed: 268 average time/residue: 1.0768 time to fit residues: 328.1707 Evaluate side-chains 240 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 23 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN C 818 HIS D 4 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17144 Z= 0.376 Angle : 0.679 12.485 23653 Z= 0.359 Chirality : 0.044 0.171 2584 Planarity : 0.004 0.035 2643 Dihedral : 22.215 179.320 3170 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 3.75 % Allowed : 25.51 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1766 helix: 0.43 (0.21), residues: 583 sheet: -2.32 (0.28), residues: 286 loop : -0.98 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 317 HIS 0.012 0.002 HIS C 818 PHE 0.016 0.002 PHE A 911 TYR 0.028 0.002 TYR A 725 ARG 0.010 0.001 ARG C 855 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 210 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7387 (t0) cc_final: 0.7153 (t0) REVERT: A 584 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7173 (p0) REVERT: A 731 ASP cc_start: 0.7505 (p0) cc_final: 0.7102 (p0) REVERT: A 743 PHE cc_start: 0.7788 (m-80) cc_final: 0.7527 (m-10) REVERT: A 877 GLU cc_start: 0.7345 (tp30) cc_final: 0.7121 (tp30) REVERT: B 52 GLN cc_start: 0.7191 (mm110) cc_final: 0.6958 (pp30) REVERT: B 219 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8574 (tt) REVERT: C 797 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: C 827 LYS cc_start: 0.8296 (tttt) cc_final: 0.7976 (tttm) REVERT: D 5 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: D 148 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7430 (mmt90) outliers start: 59 outliers final: 38 residues processed: 248 average time/residue: 1.0905 time to fit residues: 307.3021 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 485 TYR Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 23 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN D 4 GLN D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17144 Z= 0.257 Angle : 0.651 13.168 23653 Z= 0.344 Chirality : 0.043 0.384 2584 Planarity : 0.004 0.042 2643 Dihedral : 22.116 179.043 3170 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 3.12 % Allowed : 26.59 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.20), residues: 1766 helix: 0.50 (0.21), residues: 582 sheet: -2.25 (0.28), residues: 291 loop : -0.93 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 829 HIS 0.005 0.001 HIS A 766 PHE 0.022 0.002 PHE B 24 TYR 0.029 0.002 TYR A 514 ARG 0.013 0.001 ARG C 529 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7303 (t0) cc_final: 0.7070 (t0) REVERT: A 584 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7125 (p0) REVERT: A 731 ASP cc_start: 0.7413 (p0) cc_final: 0.7013 (p0) REVERT: A 743 PHE cc_start: 0.7721 (m-80) cc_final: 0.7491 (m-10) REVERT: A 877 GLU cc_start: 0.7350 (tp30) cc_final: 0.7067 (tp30) REVERT: B 52 GLN cc_start: 0.7137 (mm110) cc_final: 0.6908 (pp30) REVERT: B 89 HIS cc_start: 0.7572 (t70) cc_final: 0.7280 (t70) REVERT: B 219 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8520 (tt) REVERT: C 529 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.7034 (ttp-170) REVERT: C 797 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: C 827 LYS cc_start: 0.8282 (tttt) cc_final: 0.7968 (tttm) REVERT: D 5 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7045 (tpt) REVERT: D 242 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.6009 (tm) REVERT: D 298 GLU cc_start: 0.7030 (mp0) cc_final: 0.6804 (mp0) outliers start: 49 outliers final: 31 residues processed: 250 average time/residue: 1.1413 time to fit residues: 323.0764 Evaluate side-chains 241 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 23 ASN B 227 ASN C 637 ASN C 818 HIS D 4 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132068 restraints weight = 19783.594| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.50 r_work: 0.3508 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17144 Z= 0.248 Angle : 0.646 13.191 23653 Z= 0.341 Chirality : 0.042 0.207 2584 Planarity : 0.004 0.061 2643 Dihedral : 22.053 179.053 3170 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 3.37 % Allowed : 26.34 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1766 helix: 0.57 (0.21), residues: 581 sheet: -2.16 (0.27), residues: 310 loop : -0.90 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 829 HIS 0.005 0.001 HIS C 818 PHE 0.022 0.002 PHE B 24 TYR 0.027 0.002 TYR A 514 ARG 0.013 0.001 ARG C 529 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5938.88 seconds wall clock time: 107 minutes 20.73 seconds (6440.73 seconds total)