Starting phenix.real_space_refine (version: dev) on Tue Dec 13 17:41:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/12_2022/6xnx_22272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/12_2022/6xnx_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_22272/12_2022/6xnx_22272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/12_2022/6xnx_22272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/12_2022/6xnx_22272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnx_22272/12_2022/6xnx_22272.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 9.95, per 1000 atoms: 0.60 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: 8.11 Conformation dependent library (CDL) restraints added in 2.0 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: 6.17 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: 8.38 Time building geometry restraints manager: 8.64 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: 9193 33.58 - 67.15: 682 67.15 - 100.73: 18 100.73 - 134.30: 0 134.30 - 167.88: 3 Dihedral angle restraints: 9896 sinusoidal: 4718 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 9893 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 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. 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: 0.760 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: 4.670 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.150 Process input model: 57.230 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 19.993 167.880 6560 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.20 % Rotamer Outliers : 2.35 % 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 *********************** 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 : 1.949 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 330 average time/residue: 1.3389 time to fit residues: 492.8757 Evaluate side-chains 204 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 1 average time/residue: 0.3128 time to fit residues: 2.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 17144 Z= 0.293 Angle : 0.664 12.914 23653 Z= 0.361 Chirality : 0.044 0.147 2584 Planarity : 0.004 0.036 2643 Dihedral : 22.054 178.698 3069 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer Outliers : 5.22 % 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: -2.62 (0.18), residues: 1766 helix: -0.68 (0.20), residues: 571 sheet: -2.98 (0.24), residues: 311 loop : -1.93 (0.19), residues: 884 *********************** 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 317 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 235 time to evaluate : 1.818 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 29 residues processed: 294 average time/residue: 0.9958 time to fit residues: 336.4990 Evaluate side-chains 214 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.5199 time to fit residues: 5.4102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 135 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 818 HIS C1006 HIS D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 17144 Z= 0.238 Angle : 0.612 10.264 23653 Z= 0.333 Chirality : 0.042 0.156 2584 Planarity : 0.004 0.041 2643 Dihedral : 21.943 177.423 3069 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer Outliers : 5.73 % 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: -0.05 (0.20), residues: 582 sheet: -2.65 (0.24), residues: 343 loop : -1.54 (0.21), residues: 841 *********************** 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 319 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 229 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 36 residues processed: 292 average time/residue: 0.9881 time to fit residues: 333.9807 Evaluate side-chains 230 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 30 residues processed: 7 average time/residue: 0.2462 time to fit residues: 5.2046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 HIS D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 17144 Z= 0.309 Angle : 0.640 14.674 23653 Z= 0.343 Chirality : 0.043 0.160 2584 Planarity : 0.004 0.055 2643 Dihedral : 21.992 177.878 3069 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.85 % Rotamer Outliers : 5.60 % 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: -1.62 (0.19), residues: 1766 helix: 0.21 (0.21), residues: 584 sheet: -2.48 (0.24), residues: 349 loop : -1.28 (0.21), residues: 833 *********************** 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 304 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 216 time to evaluate : 1.860 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 41 residues processed: 273 average time/residue: 1.0016 time to fit residues: 313.9939 Evaluate side-chains 235 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 12 average time/residue: 0.3138 time to fit residues: 7.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN C 818 HIS D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2872 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= 0.274 Angle : 0.615 8.653 23653 Z= 0.332 Chirality : 0.042 0.157 2584 Planarity : 0.004 0.035 2643 Dihedral : 21.950 178.791 3069 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer Outliers : 5.03 % 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: -1.45 (0.20), residues: 1766 helix: 0.33 (0.21), residues: 584 sheet: -2.38 (0.24), residues: 347 loop : -1.16 (0.22), residues: 835 *********************** 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 294 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 215 time to evaluate : 1.761 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 43 residues processed: 270 average time/residue: 1.0191 time to fit residues: 316.4100 Evaluate side-chains 240 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 33 residues processed: 10 average time/residue: 0.3574 time to fit residues: 7.3769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 227 ASN D 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 17144 Z= 0.318 Angle : 0.632 9.231 23653 Z= 0.338 Chirality : 0.043 0.164 2584 Planarity : 0.004 0.055 2643 Dihedral : 21.977 178.752 3069 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer Outliers : 5.66 % 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: -1.26 (0.20), residues: 1766 helix: 0.42 (0.21), residues: 580 sheet: -2.27 (0.25), residues: 338 loop : -1.01 (0.22), residues: 848 *********************** 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 308 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 219 time to evaluate : 1.853 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 43 residues processed: 278 average time/residue: 1.0047 time to fit residues: 322.7118 Evaluate side-chains 236 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 1.628 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 31 residues processed: 12 average time/residue: 0.2874 time to fit residues: 7.5145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 227 ASN C 818 HIS D 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3201 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= 0.285 Angle : 0.635 11.315 23653 Z= 0.338 Chirality : 0.042 0.161 2584 Planarity : 0.004 0.034 2643 Dihedral : 21.949 179.715 3069 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer Outliers : 5.15 % 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: -1.19 (0.20), residues: 1766 helix: 0.48 (0.21), residues: 580 sheet: -2.24 (0.25), residues: 336 loop : -0.97 (0.22), residues: 850 *********************** 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 291 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 210 time to evaluate : 1.727 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 43 residues processed: 267 average time/residue: 1.0009 time to fit residues: 308.3753 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 32 residues processed: 11 average time/residue: 0.2301 time to fit residues: 6.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 1.9990 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: 1.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN D 23 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3359 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= 0.256 Angle : 0.637 13.758 23653 Z= 0.337 Chirality : 0.042 0.173 2584 Planarity : 0.004 0.051 2643 Dihedral : 21.909 179.733 3069 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.02 % Rotamer Outliers : 4.52 % 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: -1.10 (0.20), residues: 1766 helix: 0.52 (0.21), residues: 579 sheet: -2.18 (0.26), residues: 312 loop : -0.94 (0.21), residues: 875 *********************** 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 291 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 220 time to evaluate : 1.812 Fit side-chains outliers start: 71 outliers final: 43 residues processed: 272 average time/residue: 0.9495 time to fit residues: 301.1702 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 36 residues processed: 7 average time/residue: 0.3481 time to fit residues: 5.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN C 818 HIS D 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 17144 Z= 0.313 Angle : 0.647 11.816 23653 Z= 0.345 Chirality : 0.043 0.163 2584 Planarity : 0.004 0.034 2643 Dihedral : 21.935 179.997 3069 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer Outliers : 3.56 % 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: -1.09 (0.20), residues: 1766 helix: 0.50 (0.21), residues: 580 sheet: -2.16 (0.27), residues: 297 loop : -0.96 (0.21), residues: 889 *********************** 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 262 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 1.906 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 39 residues processed: 248 average time/residue: 1.0292 time to fit residues: 296.4602 Evaluate side-chains 232 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 0.2660 time to fit residues: 4.5699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 chunk 146 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN D 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17144 Z= 0.247 Angle : 0.639 11.400 23653 Z= 0.339 Chirality : 0.042 0.157 2584 Planarity : 0.004 0.039 2643 Dihedral : 21.855 178.706 3069 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer Outliers : 3.18 % 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: -1.07 (0.20), residues: 1766 helix: 0.55 (0.21), residues: 579 sheet: -2.15 (0.26), residues: 317 loop : -0.92 (0.22), residues: 870 ********************** 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 265 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 215 time to evaluate : 1.687 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 255 average time/residue: 0.9389 time to fit residues: 277.0966 Evaluate side-chains 239 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 4 average time/residue: 0.6841 time to fit residues: 5.5418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 227 ASN C 637 ASN C 818 HIS ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133265 restraints weight = 19900.135| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.51 r_work: 0.3527 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17144 Z= 0.243 Angle : 0.636 11.127 23653 Z= 0.338 Chirality : 0.042 0.160 2584 Planarity : 0.004 0.035 2643 Dihedral : 21.813 178.643 3069 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.19 % Rotamer Outliers : 3.37 % 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: -0.99 (0.20), residues: 1766 helix: 0.64 (0.21), residues: 579 sheet: -2.09 (0.26), residues: 323 loop : -0.89 (0.22), residues: 864 =============================================================================== Job complete usr+sys time: 5676.10 seconds wall clock time: 102 minutes 33.17 seconds (6153.17 seconds total)