Starting phenix.real_space_refine (version: dev) on Tue Dec 13 17:37:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/12_2022/6xnz_22274.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 884": "OD1" <-> "OD2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A TYR 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ASP 531": "OD1" <-> "OD2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C ASP 585": "OD1" <-> "OD2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ASP 774": "OD1" <-> "OD2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C ASP 864": "OD1" <-> "OD2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C ASP 884": "OD1" <-> "OD2" Residue "C ARG 894": "NH1" <-> "NH2" Residue "C PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 972": "NH1" <-> "NH2" Residue "C TYR 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ASP 306": "OD1" <-> "OD2" Residue "D PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 16544 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: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2680 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 322} 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: 4402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4402 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 523} 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: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 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: "I" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "x" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2082 SG CYS A 727 67.544 87.710 59.807 1.00 37.38 S ATOM 2103 SG CYS A 730 67.479 91.036 62.352 1.00 37.40 S ATOM 9173 SG CYS C 727 66.428 22.258 60.083 1.00 39.34 S ATOM 9194 SG CYS C 730 66.463 18.402 61.597 1.00 39.94 S Time building chain proxies: 10.19, per 1000 atoms: 0.62 Number of scatterers: 16544 At special positions: 0 Unit cell: (134.4, 111.3, 114.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 114 15.00 O 3323 8.00 N 2889 7.00 C 10112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.86 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 33.6% alpha, 9.9% beta 52 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.333A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.551A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.612A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) 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 removed outlier: 3.734A pdb=" N GLU A 901 " --> pdb=" O CYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 removed outlier: 4.418A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.895A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 4.272A pdb=" N LYS A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.841A pdb=" N MET A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1005 removed outlier: 4.598A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.918A pdb=" N SER B 314 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.816A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 580 removed outlier: 5.205A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 Processing helix chain 'C' and resid 666 through 685 Proline residue: C 674 - end of helix removed outlier: 4.100A pdb=" N SER C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 828 Processing helix chain 'C' and resid 830 through 840 Processing helix chain 'C' and resid 850 through 856 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 894 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 923 removed outlier: 4.513A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 960 through 974 removed outlier: 3.844A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.659A 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 removed outlier: 4.442A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1007 No H-bonds generated for 'chain 'C' and resid 1005 through 1007' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.538A pdb=" N ILE D 15 " --> pdb=" O ILE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 removed outlier: 4.103A pdb=" N LYS D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 597 removed outlier: 6.258A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 653 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.512A pdb=" N ARG B 73 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY B 95 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR B 77 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE B 93 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 110 removed outlier: 4.466A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 146 Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 219 removed outlier: 3.705A pdb=" N TYR B 234 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.812A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AB4, first strand: chain 'C' and resid 591 through 592 Processing sheet with id=AB5, first strand: chain 'C' and resid 594 through 603 removed outlier: 6.872A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 632 through 633 Processing sheet with id=AB7, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.539A pdb=" N PHE D 31 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.693A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AC2, first strand: chain 'D' and resid 137 through 138 removed outlier: 3.560A pdb=" N SER D 160 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AC4, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.563A pdb=" N LEU D 219 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 272 through 273 481 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 132 hydrogen bonds 264 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 6.59 Time building geometry restraints manager: 9.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.45: 7975 1.45 - 1.72: 9020 1.72 - 1.99: 160 1.99 - 2.25: 0 2.25 - 2.52: 1 Bond restraints: 17156 Sorted by residual: bond pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 1.330 2.522 -1.192 1.29e-02 6.01e+03 8.53e+03 bond pdb=" C TYR B 80 " pdb=" N LYS B 81 " ideal model delta sigma weight residual 1.332 1.231 0.101 1.40e-02 5.10e+03 5.24e+01 bond pdb=" C VAL A 759 " pdb=" O VAL A 759 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.17e-02 7.31e+03 2.10e+01 bond pdb=" C GLU C 918 " pdb=" O GLU C 918 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.18e-02 7.18e+03 1.83e+01 bond pdb=" O3' DC J 26 " pdb=" P DC J 27 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.34e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 83.13 - 98.68: 4 98.68 - 114.23: 10944 114.23 - 129.78: 12577 129.78 - 145.33: 155 145.33 - 160.88: 2 Bond angle restraints: 23682 Sorted by residual: angle pdb=" O LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 122.59 83.13 39.46 1.33e+00 5.65e-01 8.80e+02 angle pdb=" C LYS B 81 " pdb=" N HIS B 89 " pdb=" CA HIS B 89 " ideal model delta sigma weight residual 122.46 160.88 -38.42 1.41e+00 5.03e-01 7.43e+02 angle pdb=" CA LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " ideal model delta sigma weight residual 116.84 151.86 -35.02 1.71e+00 3.42e-01 4.19e+02 angle pdb=" C TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta sigma weight residual 109.65 84.04 25.61 2.07e+00 2.33e-01 1.53e+02 angle pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " pdb=" CG TYR B 80 " ideal model delta sigma weight residual 113.90 129.40 -15.50 1.80e+00 3.09e-01 7.41e+01 ... (remaining 23677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 9097 31.83 - 63.66: 760 63.66 - 95.49: 32 95.49 - 127.32: 2 127.32 - 159.15: 6 Dihedral angle restraints: 9897 sinusoidal: 4712 harmonic: 5185 Sorted by residual: dihedral pdb=" C TYR B 80 " pdb=" N TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta harmonic sigma weight residual -122.60 -87.64 -34.96 0 2.50e+00 1.60e-01 1.96e+02 dihedral pdb=" N TYR B 80 " pdb=" C TYR B 80 " pdb=" CA TYR B 80 " pdb=" CB TYR B 80 " ideal model delta harmonic sigma weight residual 122.80 98.87 23.93 0 2.50e+00 1.60e-01 9.17e+01 dihedral pdb=" CA LYS B 81 " pdb=" C LYS B 81 " pdb=" N HIS B 89 " pdb=" CA HIS B 89 " ideal model delta harmonic sigma weight residual -180.00 -134.92 -45.08 0 5.00e+00 4.00e-02 8.13e+01 ... (remaining 9894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2559 0.156 - 0.312: 25 0.312 - 0.469: 2 0.469 - 0.625: 1 0.625 - 0.781: 2 Chirality restraints: 2589 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 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA TYR B 80 " pdb=" N TYR B 80 " pdb=" C TYR B 80 " pdb=" CB TYR B 80 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA ASP C 986 " pdb=" N ASP C 986 " pdb=" C ASP C 986 " pdb=" CB ASP C 986 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 2586 not shown) Planarity restraints: 2647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 81 " -0.087 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C LYS B 81 " 0.176 2.00e-02 2.50e+03 pdb=" O LYS B 81 " -0.044 2.00e-02 2.50e+03 pdb=" N HIS B 89 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 80 " -0.098 2.00e-02 2.50e+03 5.30e-02 5.61e+01 pdb=" CG TYR B 80 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR B 80 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 80 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 80 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 80 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 80 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 80 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 80 " -0.034 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C TYR D 80 " 0.111 2.00e-02 2.50e+03 pdb=" O TYR D 80 " -0.040 2.00e-02 2.50e+03 pdb=" N LYS D 81 " -0.037 2.00e-02 2.50e+03 ... (remaining 2644 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 200 2.45 - 3.07: 12983 3.07 - 3.68: 29492 3.68 - 4.29: 43585 4.29 - 4.90: 66941 Nonbonded interactions: 153201 Sorted by model distance: nonbonded pdb=" O LEU C 729 " pdb="ZN ZN C1101 " model vdw 1.842 2.230 nonbonded pdb=" O GLN B 265 " pdb=" OG1 THR B 266 " model vdw 1.950 2.440 nonbonded pdb=" O ALA A 941 " pdb=" ND1 HIS A 942 " model vdw 2.138 2.520 nonbonded pdb=" OD1 ASP C 600 " pdb=" N4 DC I 17 " model vdw 2.198 2.520 nonbonded pdb=" ND2 ASN D 335 " pdb=" OH TYR D 344 " model vdw 2.198 2.520 ... (remaining 153196 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 459 through 1006 or (resid 1007 and (name N or name CA or \ name C or name O or name CB )) or resid 1101)) 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 338 or resid 340 thr \ ough 350)) selection = (chain 'D' and (resid 1 through 336 or (resid 337 through 338 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' and (resid 5 through 18 or resid 20 through 33)) selection = (chain 'J' and (resid 5 through 18 or resid 20 through 33)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 114 5.49 5 S 104 5.16 5 C 10112 2.51 5 N 2889 2.21 5 O 3323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.160 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: 4.730 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.150 Process input model: 55.700 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 1.192 17156 Z= 0.479 Angle : 0.965 39.456 23682 Z= 0.598 Chirality : 0.055 0.781 2589 Planarity : 0.006 0.103 2647 Dihedral : 20.537 159.149 6559 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.34 % Favored : 85.54 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -6.04 (0.14), residues: 1771 helix: -3.55 (0.15), residues: 533 sheet: -4.58 (0.26), residues: 212 loop : -4.34 (0.14), residues: 1026 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 328 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 4 residues processed: 349 average time/residue: 0.3244 time to fit residues: 163.3240 Evaluate side-chains 212 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 1.858 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1745 time to fit residues: 3.6528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 647 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS B 53 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 520 GLN ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 222 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 17156 Z= 0.258 Angle : 0.769 9.436 23682 Z= 0.406 Chirality : 0.046 0.168 2589 Planarity : 0.006 0.068 2647 Dihedral : 22.799 158.092 3084 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.77 % Favored : 89.11 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -4.42 (0.17), residues: 1773 helix: -2.11 (0.18), residues: 554 sheet: -3.78 (0.28), residues: 228 loop : -3.32 (0.17), residues: 991 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 302 average time/residue: 0.2996 time to fit residues: 135.8471 Evaluate side-chains 237 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 219 time to evaluate : 1.829 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.1636 time to fit residues: 7.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 HIS B 4 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN D 173 ASN D 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 17156 Z= 0.263 Angle : 0.714 8.333 23682 Z= 0.377 Chirality : 0.044 0.194 2589 Planarity : 0.005 0.061 2647 Dihedral : 22.771 158.334 3084 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.85 (0.17), residues: 1773 helix: -1.66 (0.19), residues: 553 sheet: -3.56 (0.28), residues: 240 loop : -2.89 (0.18), residues: 980 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 293 average time/residue: 0.3039 time to fit residues: 137.6406 Evaluate side-chains 241 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2242 time to fit residues: 9.9140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 975 ASN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 17156 Z= 0.363 Angle : 0.743 7.753 23682 Z= 0.394 Chirality : 0.046 0.230 2589 Planarity : 0.005 0.057 2647 Dihedral : 22.873 158.564 3084 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 30.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.63 (0.18), residues: 1773 helix: -1.46 (0.20), residues: 552 sheet: -3.48 (0.28), residues: 246 loop : -2.74 (0.18), residues: 975 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 270 average time/residue: 0.2801 time to fit residues: 115.9780 Evaluate side-chains 236 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1564 time to fit residues: 7.8581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 525 ASN A 750 HIS B 23 ASN B 47 HIS B 90 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN D 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 17156 Z= 0.236 Angle : 0.701 11.998 23682 Z= 0.369 Chirality : 0.043 0.196 2589 Planarity : 0.005 0.059 2647 Dihedral : 22.823 158.562 3084 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.36 (0.18), residues: 1773 helix: -1.23 (0.20), residues: 559 sheet: -3.28 (0.28), residues: 253 loop : -2.59 (0.19), residues: 961 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 264 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 281 average time/residue: 0.2856 time to fit residues: 123.1222 Evaluate side-chains 241 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1620 time to fit residues: 6.2728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 94 optimal weight: 0.0050 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 17156 Z= 0.268 Angle : 0.701 10.438 23682 Z= 0.368 Chirality : 0.044 0.251 2589 Planarity : 0.005 0.074 2647 Dihedral : 22.828 158.449 3084 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.18 (0.19), residues: 1773 helix: -0.97 (0.21), residues: 552 sheet: -3.26 (0.28), residues: 267 loop : -2.49 (0.19), residues: 954 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 252 average time/residue: 0.2750 time to fit residues: 107.4992 Evaluate side-chains 223 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1975 time to fit residues: 4.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 17156 Z= 0.346 Angle : 0.749 11.458 23682 Z= 0.389 Chirality : 0.046 0.317 2589 Planarity : 0.005 0.057 2647 Dihedral : 22.932 158.653 3084 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.19 (0.19), residues: 1773 helix: -1.00 (0.21), residues: 552 sheet: -3.26 (0.28), residues: 270 loop : -2.48 (0.19), residues: 951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 244 average time/residue: 0.2869 time to fit residues: 107.4785 Evaluate side-chains 225 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1548 time to fit residues: 6.8418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17156 Z= 0.261 Angle : 0.717 14.240 23682 Z= 0.374 Chirality : 0.044 0.261 2589 Planarity : 0.005 0.055 2647 Dihedral : 22.911 158.572 3084 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.03 (0.19), residues: 1773 helix: -0.88 (0.21), residues: 553 sheet: -3.06 (0.29), residues: 258 loop : -2.43 (0.19), residues: 962 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 254 average time/residue: 0.2822 time to fit residues: 110.1243 Evaluate side-chains 216 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1612 time to fit residues: 4.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 17156 Z= 0.247 Angle : 0.727 12.907 23682 Z= 0.377 Chirality : 0.043 0.189 2589 Planarity : 0.005 0.055 2647 Dihedral : 22.874 158.664 3084 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.93 (0.19), residues: 1773 helix: -0.79 (0.21), residues: 550 sheet: -2.94 (0.29), residues: 265 loop : -2.38 (0.19), residues: 958 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 250 average time/residue: 0.2851 time to fit residues: 109.7468 Evaluate side-chains 227 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1543 time to fit residues: 3.5720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17156 Z= 0.237 Angle : 0.722 12.906 23682 Z= 0.373 Chirality : 0.043 0.192 2589 Planarity : 0.005 0.054 2647 Dihedral : 22.858 158.846 3084 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.84 (0.19), residues: 1773 helix: -0.71 (0.21), residues: 553 sheet: -2.89 (0.29), residues: 276 loop : -2.31 (0.19), residues: 944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 238 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 244 average time/residue: 0.2806 time to fit residues: 105.9492 Evaluate side-chains 225 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1564 time to fit residues: 4.1789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.141412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.127658 restraints weight = 35224.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.129792 restraints weight = 22476.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.131337 restraints weight = 16081.142| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17156 Z= 0.242 Angle : 0.737 14.634 23682 Z= 0.378 Chirality : 0.043 0.243 2589 Planarity : 0.005 0.054 2647 Dihedral : 22.844 158.897 3084 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.76 (0.19), residues: 1773 helix: -0.64 (0.21), residues: 552 sheet: -2.77 (0.29), residues: 276 loop : -2.30 (0.19), residues: 945 =============================================================================== Job complete usr+sys time: 3077.87 seconds wall clock time: 57 minutes 41.57 seconds (3461.57 seconds total)