Starting phenix.real_space_refine (version: dev) on Tue Dec 13 18:30:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/12_2022/6xny_22273.pdb" } resolution = 2.9 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= 0.007 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 TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 531": "OD1" <-> "OD2" Residue "C ASP 546": "OD1" <-> "OD2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 551": "OD1" <-> "OD2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C ASP 573": "OD1" <-> "OD2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C ASP 774": "OD1" <-> "OD2" Residue "C GLU 824": "OE1" <-> "OE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "C ASP 864": "OD1" <-> "OD2" Residue "C GLU 877": "OE1" <-> "OE2" Residue "C TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 986": "OD1" <-> "OD2" Residue "C TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" 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: 16681 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4411 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 524} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2689 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4398 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 522} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2694 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "x" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 704 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "y" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} 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: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2082 SG CYS A 727 66.873 86.313 62.509 1.00 36.42 S ATOM 2103 SG CYS A 730 66.952 89.863 64.855 1.00 36.29 S ATOM 9178 SG CYS C 727 65.459 21.965 62.339 1.00 35.42 S ATOM 9199 SG CYS C 730 65.287 18.415 64.592 1.00 34.95 S Time building chain proxies: 10.04, per 1000 atoms: 0.60 Number of scatterers: 16681 At special positions: 0 Unit cell: (132.3, 108.15, 114.45, 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 105 16.00 P 116 15.00 Mg 4 11.99 O 3353 8.00 N 2916 7.00 C 10185 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: 8.71 Conformation dependent library (CDL) restraints added in 2.3 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 C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " Number of angles added : 4 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 22 sheets defined 35.9% alpha, 20.9% beta 58 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 6.61 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: 3.788A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.238A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) 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 777 Processing helix chain 'A' and resid 792 through 814 Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 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 907 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: 3.793A 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 1004 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.631A 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: 3.945A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.618A pdb=" N ASN C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) 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 812 Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 852 through 857 Processing helix chain 'C' and resid 859 through 868 removed outlier: 3.601A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 890 Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' 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 924 through 929 removed outlier: 3.634A pdb=" N GLU C 929 " --> pdb=" O LYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.659A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 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 534 through 536 removed outlier: 6.234A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N CYS A 652 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 626 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 601 through 603 removed outlier: 5.128A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.601A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.824A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.080A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.734A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 267 removed outlier: 7.335A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB4, first strand: chain 'C' and resid 517 through 519 removed outlier: 3.621A pdb=" N THR C 630 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 517 through 519 removed outlier: 3.621A pdb=" N THR C 630 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.029A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.469A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.326A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.941A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 270 through 273 Processing sheet with id=AC4, first strand: chain 'D' and resid 277 through 279 641 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 8.31 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2457 1.29 - 1.42: 5098 1.42 - 1.55: 9355 1.55 - 1.68: 232 1.68 - 1.81: 162 Bond restraints: 17304 Sorted by residual: bond pdb=" C PRO A 891 " pdb=" O PRO A 891 " ideal model delta sigma weight residual 1.238 1.160 0.078 1.33e-02 5.65e+03 3.44e+01 bond pdb=" C PHE A 497 " pdb=" N GLN A 498 " ideal model delta sigma weight residual 1.331 1.228 0.103 3.12e-02 1.03e+03 1.08e+01 bond pdb=" O3' DC y 45 " pdb=" P DC y 46 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.50e-02 4.44e+03 9.84e+00 bond pdb=" CA LEU A 657 " pdb=" CB LEU A 657 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.39e-02 5.18e+03 9.36e+00 bond pdb=" O3' DT M 22 " pdb=" P DG M 23 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.17e+00 ... (remaining 17299 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.31: 666 104.31 - 111.76: 8373 111.76 - 119.20: 5820 119.20 - 126.65: 8510 126.65 - 134.10: 537 Bond angle restraints: 23906 Sorted by residual: angle pdb=" N ASN D 335 " pdb=" CA ASN D 335 " pdb=" C ASN D 335 " ideal model delta sigma weight residual 111.04 99.15 11.89 1.55e+00 4.16e-01 5.89e+01 angle pdb=" O3' DC y 36 " pdb=" C3' DC y 36 " pdb=" C2' DC y 36 " ideal model delta sigma weight residual 111.50 102.11 9.39 1.50e+00 4.44e-01 3.92e+01 angle pdb=" C GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta sigma weight residual 110.17 121.40 -11.23 1.97e+00 2.58e-01 3.25e+01 angle pdb=" O3' DC x 57 " pdb=" C3' DC x 57 " pdb=" C2' DC x 57 " ideal model delta sigma weight residual 111.50 103.37 8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" CG ARG A 696 " pdb=" CD ARG A 696 " pdb=" NE ARG A 696 " ideal model delta sigma weight residual 112.00 101.67 10.33 2.20e+00 2.07e-01 2.20e+01 ... (remaining 23901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 9252 34.11 - 68.22: 693 68.22 - 102.33: 22 102.33 - 136.44: 0 136.44 - 170.55: 5 Dihedral angle restraints: 9972 sinusoidal: 4779 harmonic: 5193 Sorted by residual: dihedral pdb=" C ASN B 101 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " pdb=" CB ASN B 101 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C GLN C 520 " pdb=" N GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta harmonic sigma weight residual -122.60 -136.13 13.53 0 2.50e+00 1.60e-01 2.93e+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 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2366 0.092 - 0.185: 227 0.185 - 0.277: 11 0.277 - 0.370: 6 0.370 - 0.462: 2 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA ASN B 101 " pdb=" N ASN B 101 " pdb=" C ASN B 101 " pdb=" CB ASN B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA GLN C 520 " pdb=" N GLN C 520 " pdb=" C GLN C 520 " pdb=" CB GLN C 520 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+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 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 2609 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " 0.313 9.50e-02 1.11e+02 1.40e-01 1.21e+01 pdb=" NE ARG A 773 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y 30 " 0.043 2.00e-02 2.50e+03 1.93e-02 1.02e+01 pdb=" N9 DA y 30 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA y 30 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA y 30 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA y 30 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA y 30 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA y 30 " 0.020 2.00e-02 2.50e+03 pdb=" N1 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA y 30 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA y 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT x 43 " 0.038 2.00e-02 2.50e+03 1.76e-02 7.78e+00 pdb=" N1 DT x 43 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT x 43 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT x 43 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT x 43 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT x 43 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT x 43 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT x 43 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT x 43 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT x 43 " -0.009 2.00e-02 2.50e+03 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 31 2.28 - 2.93: 8234 2.93 - 3.59: 28144 3.59 - 4.24: 49319 4.24 - 4.90: 76973 Nonbonded interactions: 162701 Sorted by model distance: nonbonded pdb=" O GLY A 601 " pdb="MG MG A1101 " model vdw 1.619 2.170 nonbonded pdb=" OE2 GLU C 662 " pdb="MG MG C1102 " model vdw 1.816 2.170 nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1102 " model vdw 1.898 2.170 nonbonded pdb=" OP2 DC x 47 " pdb="MG MG C1101 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1101 " model vdw 2.080 2.170 ... (remaining 162696 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 1006 or (resid 1007 and (name N or name CA or \ name C or name O or name CB )) or resid 1101 through 1103)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 116 or (resid 117 through 118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 119 through 350)) selection = (chain 'D' and (resid 1 through 336 or (resid 337 through 339 and (name N or nam \ e CA or name C or name O or name CB )) or resid 340 through 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'x' and ((resid 35 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N9 or name C8 or name N7 or \ name C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C4 )) or \ resid 36 through 48 or resid 50 through 65)) selection = (chain 'y' and (resid 24 through 37 or resid 39 through 54)) } 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 116 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 10185 2.51 5 N 2916 2.21 5 O 3353 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: 0.450 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: 4.740 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.160 Process input model: 59.910 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.011 0.103 17304 Z= 0.675 Angle : 0.823 11.892 23906 Z= 0.488 Chirality : 0.056 0.462 2612 Planarity : 0.005 0.140 2655 Dihedral : 20.594 170.550 6628 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.93 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.16), residues: 1775 helix: -2.62 (0.16), residues: 573 sheet: -3.59 (0.23), residues: 322 loop : -2.99 (0.18), residues: 880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 349 average time/residue: 1.1479 time to fit residues: 451.6503 Evaluate side-chains 227 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.9489 time to fit residues: 4.6085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 633 HIS A 740 ASN A 990 HIS B 33 GLN B 232 ASN B 282 GLN C 609 HIS C 820 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 17304 Z= 0.277 Angle : 0.682 8.240 23906 Z= 0.368 Chirality : 0.044 0.173 2612 Planarity : 0.004 0.046 2655 Dihedral : 22.420 174.298 3142 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.18), residues: 1775 helix: -1.08 (0.19), residues: 590 sheet: -3.31 (0.24), residues: 340 loop : -1.91 (0.21), residues: 845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 250 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 29 residues processed: 304 average time/residue: 0.9829 time to fit residues: 344.3013 Evaluate side-chains 235 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.007 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.2029 time to fit residues: 4.6407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN D 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 17304 Z= 0.359 Angle : 0.682 8.784 23906 Z= 0.364 Chirality : 0.044 0.181 2612 Planarity : 0.004 0.042 2655 Dihedral : 22.543 177.969 3142 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.03 % Rotamer Outliers : 5.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1775 helix: -0.55 (0.19), residues: 588 sheet: -2.94 (0.25), residues: 321 loop : -1.61 (0.21), residues: 866 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 230 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 39 residues processed: 292 average time/residue: 1.0602 time to fit residues: 353.5069 Evaluate side-chains 237 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.7529 time to fit residues: 9.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 753 ASN C 914 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.266 Angle : 0.648 10.997 23906 Z= 0.346 Chirality : 0.042 0.169 2612 Planarity : 0.004 0.042 2655 Dihedral : 22.416 175.724 3142 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 1775 helix: -0.21 (0.20), residues: 588 sheet: -2.90 (0.24), residues: 336 loop : -1.41 (0.21), residues: 851 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 239 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 39 residues processed: 289 average time/residue: 1.0342 time to fit residues: 343.7259 Evaluate side-chains 243 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 29 residues processed: 10 average time/residue: 0.4939 time to fit residues: 8.7917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN D 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 17304 Z= 0.264 Angle : 0.637 10.992 23906 Z= 0.342 Chirality : 0.042 0.164 2612 Planarity : 0.004 0.034 2655 Dihedral : 22.351 175.861 3142 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer Outliers : 5.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.19), residues: 1775 helix: -0.02 (0.20), residues: 588 sheet: -2.77 (0.24), residues: 333 loop : -1.26 (0.22), residues: 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 226 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 48 residues processed: 281 average time/residue: 0.9625 time to fit residues: 312.7577 Evaluate side-chains 261 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.071 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.7060 time to fit residues: 13.7137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.233 Angle : 0.621 7.704 23906 Z= 0.335 Chirality : 0.041 0.165 2612 Planarity : 0.004 0.033 2655 Dihedral : 22.243 175.384 3142 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1775 helix: 0.17 (0.21), residues: 589 sheet: -2.62 (0.25), residues: 336 loop : -1.17 (0.22), residues: 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 244 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 45 residues processed: 295 average time/residue: 1.0034 time to fit residues: 342.8123 Evaluate side-chains 259 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 214 time to evaluate : 1.865 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 35 residues processed: 10 average time/residue: 0.4624 time to fit residues: 8.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 103 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17304 Z= 0.217 Angle : 0.622 10.508 23906 Z= 0.334 Chirality : 0.041 0.166 2612 Planarity : 0.004 0.033 2655 Dihedral : 22.163 175.172 3142 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1775 helix: 0.24 (0.21), residues: 596 sheet: -2.48 (0.25), residues: 348 loop : -1.04 (0.22), residues: 831 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 240 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 46 residues processed: 288 average time/residue: 1.0214 time to fit residues: 337.8866 Evaluate side-chains 259 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 39 residues processed: 8 average time/residue: 0.5882 time to fit residues: 8.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN B 16 GLN B 265 GLN B 278 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.229 Angle : 0.626 9.075 23906 Z= 0.334 Chirality : 0.042 0.255 2612 Planarity : 0.004 0.035 2655 Dihedral : 22.142 175.288 3142 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.82 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1775 helix: 0.32 (0.21), residues: 594 sheet: -2.33 (0.25), residues: 352 loop : -0.94 (0.22), residues: 829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 43 residues processed: 278 average time/residue: 0.9407 time to fit residues: 303.5989 Evaluate side-chains 253 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 6 average time/residue: 0.4935 time to fit residues: 6.3300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 158 optimal weight: 0.0070 chunk 110 optimal weight: 0.5980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 265 GLN C 482 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.252 Angle : 0.631 9.213 23906 Z= 0.337 Chirality : 0.042 0.162 2612 Planarity : 0.004 0.034 2655 Dihedral : 22.164 175.352 3142 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1775 helix: 0.31 (0.20), residues: 594 sheet: -2.27 (0.25), residues: 353 loop : -0.93 (0.22), residues: 828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 45 residues processed: 263 average time/residue: 0.9783 time to fit residues: 299.1364 Evaluate side-chains 246 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 8 average time/residue: 0.7310 time to fit residues: 9.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 17304 Z= 0.395 Angle : 0.698 9.036 23906 Z= 0.370 Chirality : 0.046 0.184 2612 Planarity : 0.004 0.044 2655 Dihedral : 22.473 176.694 3142 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1775 helix: 0.03 (0.20), residues: 594 sheet: -2.19 (0.27), residues: 322 loop : -1.03 (0.22), residues: 859 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 41 residues processed: 251 average time/residue: 1.0567 time to fit residues: 305.3603 Evaluate side-chains 243 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 7 average time/residue: 0.4849 time to fit residues: 6.9675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 282 GLN C 914 GLN ** D 207 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 = 0.3923 r_free = 0.3923 target = 0.158800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137261 restraints weight = 20950.295| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.42 r_work: 0.3554 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 17304 Z= 0.236 Angle : 0.642 9.969 23906 Z= 0.341 Chirality : 0.043 0.181 2612 Planarity : 0.004 0.040 2655 Dihedral : 22.195 174.089 3142 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.82 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1775 helix: 0.18 (0.20), residues: 594 sheet: -2.21 (0.26), residues: 330 loop : -0.93 (0.22), residues: 851 =============================================================================== Job complete usr+sys time: 5685.35 seconds wall clock time: 102 minutes 38.55 seconds (6158.55 seconds total)