Starting phenix.real_space_refine on Fri Feb 16 22:21:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/02_2024/6xny_22273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/02_2024/6xny_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_22273/02_2024/6xny_22273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/02_2024/6xny_22273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/02_2024/6xny_22273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xny_22273/02_2024/6xny_22273.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.09, per 1000 atoms: 0.54 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: 7.84 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN 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: 6.30 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: 7.37 Time building geometry restraints manager: 8.35 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: 9335 34.11 - 68.22: 708 68.22 - 102.33: 22 102.33 - 136.44: 0 136.44 - 170.55: 5 Dihedral angle restraints: 10070 sinusoidal: 4877 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 10067 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 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: 0.750 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: 0.030 Extract box with map and model: 4.070 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 56.570 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 20.646 170.550 6726 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.93 % Rotamer: Outliers : 3.25 % Allowed : 13.70 % Favored : 83.05 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 893 HIS 0.012 0.001 HIS C 937 PHE 0.015 0.002 PHE B 206 TYR 0.030 0.002 TYR D 195 ARG 0.006 0.001 ARG B 159 *********************** 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 : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 1 MET cc_start: 0.4432 (OUTLIER) cc_final: 0.3937 (ptm) REVERT: B 186 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6690 (p0) REVERT: C 724 VAL cc_start: 0.8544 (p) cc_final: 0.8266 (m) REVERT: D 20 SER cc_start: 0.8237 (m) cc_final: 0.7759 (p) REVERT: D 80 TYR cc_start: 0.6675 (m-80) cc_final: 0.6471 (m-80) REVERT: D 164 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7404 (p) REVERT: D 234 TYR cc_start: 0.7776 (m-80) cc_final: 0.7562 (m-80) outliers start: 51 outliers final: 25 residues processed: 349 average time/residue: 1.2460 time to fit residues: 487.0456 Evaluate side-chains 234 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 205 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 146 optimal weight: 0.0770 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: 0.5938 ------------------------------------------------------------------------------- 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 265 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17304 Z= 0.252 Angle : 0.672 8.159 23906 Z= 0.363 Chirality : 0.043 0.175 2612 Planarity : 0.004 0.044 2655 Dihedral : 22.403 173.561 3279 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.40 % Allowed : 19.50 % Favored : 76.10 % 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: -2.89 (0.18), residues: 1775 helix: -1.01 (0.19), residues: 586 sheet: -3.30 (0.24), residues: 338 loop : -1.88 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 992 HIS 0.009 0.001 HIS C 942 PHE 0.016 0.002 PHE C 591 TYR 0.019 0.002 TYR D 234 ARG 0.009 0.001 ARG C 855 *********************** 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 332 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 263 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6994 (mm-40) REVERT: A 572 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5988 (tt0) REVERT: A 709 GLU cc_start: 0.7732 (tt0) cc_final: 0.7481 (tt0) REVERT: B 1 MET cc_start: 0.4848 (ptt) cc_final: 0.4493 (ptm) REVERT: B 186 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6852 (p0) REVERT: B 237 ARG cc_start: 0.7666 (tpp-160) cc_final: 0.7454 (ttm110) REVERT: B 288 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8834 (p) REVERT: C 847 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6750 (ttp) REVERT: C 877 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: C 883 MET cc_start: 0.8342 (tpp) cc_final: 0.8037 (tpp) REVERT: D 20 SER cc_start: 0.8129 (m) cc_final: 0.7670 (p) outliers start: 69 outliers final: 20 residues processed: 305 average time/residue: 1.0460 time to fit residues: 364.1260 Evaluate side-chains 236 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 877 GLU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17304 Z= 0.386 Angle : 0.688 9.029 23906 Z= 0.368 Chirality : 0.045 0.284 2612 Planarity : 0.004 0.042 2655 Dihedral : 22.575 177.938 3250 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 4.40 % Allowed : 22.37 % Favored : 73.23 % 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: -2.43 (0.19), residues: 1775 helix: -0.61 (0.19), residues: 591 sheet: -3.10 (0.23), residues: 354 loop : -1.53 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 956 HIS 0.005 0.001 HIS A 515 PHE 0.017 0.002 PHE C 804 TYR 0.021 0.002 TYR C 886 ARG 0.007 0.001 ARG C 855 *********************** 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 305 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 236 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: A 768 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8528 (m) REVERT: A 774 ASP cc_start: 0.7282 (t70) cc_final: 0.7064 (t0) REVERT: B 1 MET cc_start: 0.4851 (ptt) cc_final: 0.4517 (ptm) REVERT: C 828 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7193 (mtp85) REVERT: C 843 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (pp) REVERT: D 195 TYR cc_start: 0.8125 (m-80) cc_final: 0.7742 (m-80) outliers start: 69 outliers final: 32 residues processed: 281 average time/residue: 1.1285 time to fit residues: 359.7874 Evaluate side-chains 237 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 913 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 473 ASN C 482 HIS C 753 ASN C 914 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 17304 Z= 0.499 Angle : 0.748 11.269 23906 Z= 0.395 Chirality : 0.047 0.260 2612 Planarity : 0.005 0.039 2655 Dihedral : 22.819 177.219 3245 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 5.10 % Allowed : 23.52 % Favored : 71.38 % 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: -2.29 (0.19), residues: 1775 helix: -0.58 (0.19), residues: 597 sheet: -2.87 (0.25), residues: 311 loop : -1.59 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 992 HIS 0.007 0.002 HIS D 207 PHE 0.018 0.002 PHE C 698 TYR 0.023 0.002 TYR C 725 ARG 0.007 0.001 ARG A 855 *********************** 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 304 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 224 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5954 (tt0) REVERT: A 642 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 667 THR cc_start: 0.8883 (m) cc_final: 0.8634 (m) REVERT: A 690 GLU cc_start: 0.7593 (pp20) cc_final: 0.7369 (pm20) REVERT: A 774 ASP cc_start: 0.7515 (t70) cc_final: 0.7238 (t0) REVERT: A 985 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: B 1 MET cc_start: 0.5035 (ptt) cc_final: 0.4604 (ptm) REVERT: B 143 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: C 584 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6513 (p0) REVERT: C 661 ASP cc_start: 0.7209 (t0) cc_final: 0.6977 (t0) REVERT: C 828 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: C 843 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8207 (pp) REVERT: C 847 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7023 (ttp) REVERT: D 80 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5930 (m-80) outliers start: 80 outliers final: 33 residues processed: 271 average time/residue: 1.1330 time to fit residues: 348.9544 Evaluate side-chains 239 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 934 ASN Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 815 VAL Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 847 MET Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 154 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 162 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 278 GLN C 914 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17304 Z= 0.246 Angle : 0.652 8.284 23906 Z= 0.349 Chirality : 0.042 0.206 2612 Planarity : 0.004 0.037 2655 Dihedral : 22.470 174.769 3244 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 4.72 % Allowed : 24.60 % Favored : 70.68 % 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: -1.97 (0.19), residues: 1775 helix: -0.15 (0.20), residues: 592 sheet: -2.90 (0.24), residues: 333 loop : -1.36 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 956 HIS 0.005 0.001 HIS D 47 PHE 0.016 0.002 PHE D 271 TYR 0.019 0.002 TYR C 886 ARG 0.010 0.001 ARG C 855 *********************** 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 303 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 229 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: A 572 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5818 (tt0) REVERT: A 690 GLU cc_start: 0.7443 (pp20) cc_final: 0.7207 (pm20) REVERT: A 774 ASP cc_start: 0.7347 (t70) cc_final: 0.7088 (t0) REVERT: A 935 TYR cc_start: 0.7978 (m-10) cc_final: 0.7754 (m-10) REVERT: B 1 MET cc_start: 0.5085 (ptt) cc_final: 0.4715 (ptm) REVERT: B 143 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: C 828 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7175 (mtp85) REVERT: C 843 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8005 (pp) REVERT: C 914 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7338 (mm110) REVERT: D 80 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5612 (m-80) REVERT: D 279 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7487 (pt) outliers start: 74 outliers final: 33 residues processed: 275 average time/residue: 1.0965 time to fit residues: 342.8849 Evaluate side-chains 246 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 205 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3325 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= 0.250 Angle : 0.641 8.214 23906 Z= 0.343 Chirality : 0.042 0.177 2612 Planarity : 0.004 0.034 2655 Dihedral : 22.369 175.044 3241 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 4.33 % Allowed : 25.37 % Favored : 70.30 % 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: -1.69 (0.19), residues: 1775 helix: 0.06 (0.21), residues: 593 sheet: -2.62 (0.25), residues: 316 loop : -1.28 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 956 HIS 0.004 0.001 HIS D 47 PHE 0.018 0.002 PHE B 271 TYR 0.018 0.002 TYR C 514 ARG 0.010 0.001 ARG C 855 *********************** 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 283 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 215 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: A 690 GLU cc_start: 0.7450 (pp20) cc_final: 0.7229 (pm20) REVERT: A 774 ASP cc_start: 0.7283 (t70) cc_final: 0.7043 (t0) REVERT: A 935 TYR cc_start: 0.7968 (m-10) cc_final: 0.7741 (m-10) REVERT: B 1 MET cc_start: 0.5177 (ptt) cc_final: 0.4790 (ptm) REVERT: B 143 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: C 699 LYS cc_start: 0.8197 (mttp) cc_final: 0.7984 (mmtt) REVERT: C 828 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7234 (mtp85) REVERT: C 843 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8022 (pp) REVERT: C 904 GLU cc_start: 0.6397 (pm20) cc_final: 0.6069 (pm20) REVERT: D 237 ARG cc_start: 0.7076 (ttm110) cc_final: 0.6625 (ttm110) outliers start: 68 outliers final: 35 residues processed: 264 average time/residue: 1.0695 time to fit residues: 322.9104 Evaluate side-chains 244 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 205 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 310 ASP Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 473 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17304 Z= 0.343 Angle : 0.665 8.410 23906 Z= 0.354 Chirality : 0.044 0.175 2612 Planarity : 0.004 0.034 2655 Dihedral : 22.499 176.009 3241 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 4.40 % Allowed : 25.56 % Favored : 70.04 % 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: -1.61 (0.19), residues: 1775 helix: 0.07 (0.20), residues: 590 sheet: -2.48 (0.26), residues: 318 loop : -1.23 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 992 HIS 0.006 0.001 HIS B 140 PHE 0.019 0.002 PHE B 271 TYR 0.019 0.002 TYR C 928 ARG 0.008 0.001 ARG D 159 *********************** 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 291 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 222 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: A 690 GLU cc_start: 0.7475 (pp20) cc_final: 0.7193 (pm20) REVERT: A 774 ASP cc_start: 0.7418 (t70) cc_final: 0.7189 (t0) REVERT: A 935 TYR cc_start: 0.8071 (m-10) cc_final: 0.7844 (m-10) REVERT: B 1 MET cc_start: 0.5263 (ptt) cc_final: 0.4827 (ptm) REVERT: B 143 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 828 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7255 (mtp85) REVERT: C 843 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (pp) REVERT: C 848 MET cc_start: 0.7104 (mpp) cc_final: 0.6831 (mpp) REVERT: C 904 GLU cc_start: 0.6491 (pm20) cc_final: 0.6100 (pm20) outliers start: 69 outliers final: 40 residues processed: 262 average time/residue: 1.0847 time to fit residues: 323.5053 Evaluate side-chains 251 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 914 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17304 Z= 0.254 Angle : 0.642 9.574 23906 Z= 0.342 Chirality : 0.042 0.160 2612 Planarity : 0.004 0.033 2655 Dihedral : 22.360 174.865 3241 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.46 % Favored : 94.48 % Rotamer: Outliers : 4.46 % Allowed : 25.94 % Favored : 69.60 % 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: -1.55 (0.20), residues: 1775 helix: 0.13 (0.20), residues: 592 sheet: -2.66 (0.25), residues: 324 loop : -1.09 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 992 HIS 0.006 0.001 HIS B 47 PHE 0.019 0.002 PHE B 271 TYR 0.019 0.002 TYR C 928 ARG 0.009 0.001 ARG C 855 *********************** 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 291 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 221 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: A 690 GLU cc_start: 0.7342 (pp20) cc_final: 0.6972 (pm20) REVERT: A 774 ASP cc_start: 0.7381 (t70) cc_final: 0.7142 (t0) REVERT: A 935 TYR cc_start: 0.7967 (m-10) cc_final: 0.7751 (m-10) REVERT: B 1 MET cc_start: 0.5298 (ptt) cc_final: 0.4896 (ptm) REVERT: B 143 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: C 699 LYS cc_start: 0.8206 (mttp) cc_final: 0.7914 (mmtt) REVERT: C 828 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7258 (mtp85) REVERT: C 843 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8066 (pp) REVERT: C 848 MET cc_start: 0.6950 (mpp) cc_final: 0.6712 (mpp) REVERT: C 904 GLU cc_start: 0.6408 (pm20) cc_final: 0.6048 (pm20) REVERT: C 963 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8340 (m) REVERT: D 80 TYR cc_start: 0.5691 (OUTLIER) cc_final: 0.4914 (m-10) REVERT: D 237 ARG cc_start: 0.6998 (ttm110) cc_final: 0.6509 (ttm110) outliers start: 70 outliers final: 38 residues processed: 265 average time/residue: 1.0652 time to fit residues: 322.3823 Evaluate side-chains 252 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 158 optimal weight: 0.0170 chunk 110 optimal weight: 0.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 647 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17304 Z= 0.239 Angle : 0.632 9.902 23906 Z= 0.338 Chirality : 0.042 0.161 2612 Planarity : 0.004 0.040 2655 Dihedral : 22.275 174.682 3241 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 3.25 % Allowed : 27.47 % Favored : 69.28 % 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: -1.45 (0.20), residues: 1775 helix: 0.19 (0.21), residues: 594 sheet: -2.61 (0.25), residues: 321 loop : -1.01 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 893 HIS 0.007 0.001 HIS D 207 PHE 0.019 0.002 PHE B 271 TYR 0.019 0.002 TYR C 928 ARG 0.009 0.001 ARG C 855 *********************** 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 277 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 226 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: A 690 GLU cc_start: 0.7316 (pp20) cc_final: 0.6873 (pm20) REVERT: A 709 GLU cc_start: 0.7743 (tt0) cc_final: 0.7508 (tt0) REVERT: A 774 ASP cc_start: 0.7328 (t70) cc_final: 0.7097 (t0) REVERT: A 935 TYR cc_start: 0.7951 (m-10) cc_final: 0.7739 (m-10) REVERT: B 1 MET cc_start: 0.5323 (ptt) cc_final: 0.4926 (ptm) REVERT: B 143 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: C 602 MET cc_start: 0.7283 (mtp) cc_final: 0.7060 (ttm) REVERT: C 828 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7330 (mtp85) REVERT: C 843 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8089 (pp) REVERT: C 963 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8272 (m) REVERT: D 1 MET cc_start: 0.6889 (mtp) cc_final: 0.6147 (mtt) REVERT: D 80 TYR cc_start: 0.5510 (OUTLIER) cc_final: 0.4818 (m-10) outliers start: 51 outliers final: 31 residues processed: 259 average time/residue: 1.0367 time to fit residues: 307.5836 Evaluate side-chains 244 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR 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: 0.2980 chunk 123 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 171 optimal weight: 0.0470 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17304 Z= 0.253 Angle : 0.635 8.513 23906 Z= 0.339 Chirality : 0.042 0.161 2612 Planarity : 0.004 0.064 2655 Dihedral : 22.257 174.748 3241 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.82 % Rotamer: Outliers : 3.19 % Allowed : 27.60 % Favored : 69.22 % 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: -1.37 (0.20), residues: 1775 helix: 0.22 (0.20), residues: 597 sheet: -2.44 (0.25), residues: 338 loop : -0.95 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 893 HIS 0.014 0.001 HIS D 207 PHE 0.020 0.002 PHE B 271 TYR 0.021 0.002 TYR C 928 ARG 0.013 0.001 ARG D 237 ********************** 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 273 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 223 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: A 709 GLU cc_start: 0.7752 (tt0) cc_final: 0.7516 (tt0) REVERT: A 774 ASP cc_start: 0.7326 (t70) cc_final: 0.7099 (t0) REVERT: A 935 TYR cc_start: 0.7960 (m-10) cc_final: 0.7735 (m-10) REVERT: B 1 MET cc_start: 0.5328 (ptt) cc_final: 0.4894 (ptm) REVERT: B 143 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: B 152 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7922 (ttp) REVERT: C 828 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7275 (mtp85) REVERT: C 843 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8048 (pp) REVERT: C 927 ARG cc_start: 0.7220 (mtp85) cc_final: 0.7010 (ttm-80) REVERT: C 963 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8263 (m) REVERT: D 1 MET cc_start: 0.6893 (mtp) cc_final: 0.6145 (mtt) REVERT: D 80 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4702 (m-10) outliers start: 50 outliers final: 32 residues processed: 253 average time/residue: 1.1376 time to fit residues: 326.1904 Evaluate side-chains 252 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 883 MET Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 ASN B 265 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137774 restraints weight = 21338.537| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.43 r_work: 0.3556 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17304 Z= 0.242 Angle : 0.630 8.898 23906 Z= 0.338 Chirality : 0.042 0.162 2612 Planarity : 0.004 0.064 2655 Dihedral : 22.216 174.572 3241 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 3.06 % Allowed : 27.79 % Favored : 69.15 % 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: -1.32 (0.20), residues: 1775 helix: 0.25 (0.21), residues: 593 sheet: -2.33 (0.25), residues: 338 loop : -0.95 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 893 HIS 0.013 0.001 HIS D 207 PHE 0.028 0.002 PHE D 271 TYR 0.020 0.002 TYR C 928 ARG 0.012 0.001 ARG D 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6012.06 seconds wall clock time: 108 minutes 11.32 seconds (6491.32 seconds total)