Starting phenix.real_space_refine on Fri Feb 16 20:58:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/02_2024/6xnz_22274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/02_2024/6xnz_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_22274/02_2024/6xnz_22274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/02_2024/6xnz_22274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/02_2024/6xnz_22274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xnz_22274/02_2024/6xnz_22274.pdb" } resolution = 3.8 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= 0.005 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 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. 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-5238/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: 9.15, per 1000 atoms: 0.55 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: 8.23 Conformation dependent library (CDL) restraints added in 2.7 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: 6.40 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: 6.80 Time building geometry restraints manager: 8.71 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: 9178 31.83 - 63.66: 775 63.66 - 95.49: 32 95.49 - 127.32: 2 127.32 - 159.15: 6 Dihedral angle restraints: 9993 sinusoidal: 4808 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 9990 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 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: 0.850 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: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 56.400 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.966 39.456 23682 Z= 0.598 Chirality : 0.055 0.781 2589 Planarity : 0.006 0.103 2647 Dihedral : 20.609 159.149 6655 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.34 % Favored : 85.54 % Rotamer: Outliers : 1.72 % Allowed : 4.73 % Favored : 93.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 317 HIS 0.007 0.001 HIS D 94 PHE 0.018 0.002 PHE D 206 TYR 0.103 0.003 TYR B 80 ARG 0.013 0.001 ARG D 159 *********************** 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 : 1.694 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 REVERT: A 773 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6784 (ttt180) REVERT: A 916 PHE cc_start: 0.7639 (t80) cc_final: 0.7223 (t80) REVERT: A 926 TYR cc_start: 0.7492 (p90) cc_final: 0.4030 (p90) REVERT: B 102 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: B 172 TRP cc_start: 0.8207 (t-100) cc_final: 0.7689 (t-100) REVERT: B 321 ASN cc_start: 0.7536 (p0) cc_final: 0.7237 (p0) REVERT: C 859 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.7195 (p) REVERT: D 159 ARG cc_start: 0.7414 (ptp-110) cc_final: 0.7046 (ptp-170) REVERT: D 206 PHE cc_start: 0.7463 (m-80) cc_final: 0.7258 (m-80) outliers start: 27 outliers final: 4 residues processed: 349 average time/residue: 0.3298 time to fit residues: 164.8604 Evaluate side-chains 218 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 211 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 859 THR 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: 0.8980 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 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: 0.8980 ------------------------------------------------------------------------------- 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: 0.7014 moved from start: 0.2120 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= 0.256 Angle : 0.754 9.702 23682 Z= 0.400 Chirality : 0.045 0.169 2589 Planarity : 0.006 0.071 2647 Dihedral : 22.913 157.911 3194 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.77 % Favored : 89.17 % Rotamer: Outliers : 1.85 % Allowed : 14.56 % Favored : 83.59 % 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: -4.46 (0.17), residues: 1773 helix: -2.14 (0.18), residues: 549 sheet: -3.81 (0.28), residues: 228 loop : -3.34 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 829 HIS 0.009 0.002 HIS B 313 PHE 0.024 0.002 PHE C 557 TYR 0.034 0.002 TYR B 80 ARG 0.012 0.001 ARG D 73 *********************** 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 311 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 282 time to evaluate : 1.678 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 REVERT: A 485 TYR cc_start: 0.7647 (t80) cc_final: 0.7167 (t80) REVERT: A 658 MET cc_start: 0.7624 (mpp) cc_final: 0.6937 (mtm) REVERT: A 858 MET cc_start: 0.7446 (mmt) cc_final: 0.7061 (mmt) REVERT: A 886 TYR cc_start: 0.6755 (t80) cc_final: 0.6401 (t80) REVERT: A 916 PHE cc_start: 0.7267 (t80) cc_final: 0.6929 (t80) REVERT: A 974 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5879 (ptm) REVERT: A 994 TYR cc_start: 0.8033 (t80) cc_final: 0.7442 (t80) REVERT: B 102 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: C 711 LEU cc_start: 0.8836 (tt) cc_final: 0.8455 (tt) REVERT: C 841 MET cc_start: 0.3759 (mmp) cc_final: 0.3537 (mmp) REVERT: C 848 MET cc_start: 0.6975 (mmm) cc_final: 0.6412 (mmt) REVERT: D 46 PHE cc_start: 0.7756 (m-80) cc_final: 0.7506 (m-80) REVERT: D 173 ASN cc_start: 0.8298 (m-40) cc_final: 0.8068 (m110) REVERT: D 206 PHE cc_start: 0.7193 (m-80) cc_final: 0.6939 (m-80) outliers start: 29 outliers final: 18 residues processed: 304 average time/residue: 0.3094 time to fit residues: 139.6995 Evaluate side-chains 243 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 760 TRP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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** ** D 16 GLN ** 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: 0.7192 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17156 Z= 0.370 Angle : 0.759 7.797 23682 Z= 0.403 Chirality : 0.046 0.287 2589 Planarity : 0.006 0.062 2647 Dihedral : 22.983 158.625 3184 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 29.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 3.32 % Allowed : 18.52 % Favored : 78.16 % 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: -4.10 (0.17), residues: 1773 helix: -1.83 (0.19), residues: 551 sheet: -3.64 (0.27), residues: 251 loop : -3.08 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 829 HIS 0.008 0.002 HIS C 766 PHE 0.023 0.003 PHE C 557 TYR 0.022 0.002 TYR B 80 ARG 0.009 0.001 ARG A 972 *********************** 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 293 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 241 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 LEU cc_start: 0.8225 (mt) cc_final: 0.7897 (mt) REVERT: A 658 MET cc_start: 0.7997 (mpp) cc_final: 0.7737 (mpp) REVERT: A 711 LEU cc_start: 0.8607 (tt) cc_final: 0.8343 (tt) REVERT: A 858 MET cc_start: 0.7470 (mmt) cc_final: 0.6647 (mmt) REVERT: B 94 HIS cc_start: 0.6688 (t-90) cc_final: 0.6447 (t-170) REVERT: B 146 TYR cc_start: 0.6400 (m-10) cc_final: 0.6180 (m-10) REVERT: C 972 ARG cc_start: 0.7479 (ptm-80) cc_final: 0.7220 (ptm160) REVERT: D 73 ARG cc_start: 0.7048 (ptt-90) cc_final: 0.6839 (ptt-90) REVERT: D 162 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7928 (mpp) REVERT: D 206 PHE cc_start: 0.7355 (m-80) cc_final: 0.7089 (m-80) REVERT: D 299 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7695 (mp) outliers start: 52 outliers final: 28 residues processed: 280 average time/residue: 0.2781 time to fit residues: 117.5283 Evaluate side-chains 235 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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** ** 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 515 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17156 Z= 0.305 Angle : 0.718 7.677 23682 Z= 0.381 Chirality : 0.044 0.199 2589 Planarity : 0.005 0.058 2647 Dihedral : 22.922 158.561 3180 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 28.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.45 % Allowed : 21.46 % Favored : 75.10 % 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: -3.75 (0.18), residues: 1773 helix: -1.56 (0.19), residues: 555 sheet: -3.50 (0.28), residues: 243 loop : -2.84 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 829 HIS 0.013 0.001 HIS A 515 PHE 0.028 0.002 PHE A 916 TYR 0.018 0.002 TYR D 68 ARG 0.010 0.001 ARG A 972 *********************** 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 293 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 239 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 LEU cc_start: 0.8132 (mt) cc_final: 0.7824 (mt) REVERT: A 658 MET cc_start: 0.8247 (mpp) cc_final: 0.7344 (mpp) REVERT: A 773 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7212 (ptm160) REVERT: A 858 MET cc_start: 0.7587 (mmt) cc_final: 0.6728 (mmt) REVERT: A 916 PHE cc_start: 0.7645 (t80) cc_final: 0.7426 (t80) REVERT: A 949 ARG cc_start: 0.7614 (tmm-80) cc_final: 0.7378 (tmm-80) REVERT: A 956 TRP cc_start: 0.8432 (m100) cc_final: 0.7986 (m100) REVERT: B 94 HIS cc_start: 0.6768 (t-90) cc_final: 0.6537 (t-170) REVERT: B 196 ILE cc_start: 0.6496 (tp) cc_final: 0.6212 (tp) REVERT: B 197 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7208 (mm) REVERT: C 466 VAL cc_start: 0.8165 (t) cc_final: 0.7839 (p) REVERT: C 690 GLU cc_start: 0.4547 (pm20) cc_final: 0.4172 (pm20) REVERT: C 849 MET cc_start: 0.6077 (tpt) cc_final: 0.5836 (tpp) REVERT: C 972 ARG cc_start: 0.7429 (ptm-80) cc_final: 0.7136 (ptm-80) REVERT: D 16 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: D 206 PHE cc_start: 0.7283 (m-80) cc_final: 0.7042 (m-80) REVERT: D 299 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7614 (mp) outliers start: 54 outliers final: 33 residues processed: 277 average time/residue: 0.2790 time to fit residues: 117.6727 Evaluate side-chains 246 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 525 ASN B 47 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3524 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= 0.217 Angle : 0.677 12.560 23682 Z= 0.359 Chirality : 0.043 0.173 2589 Planarity : 0.005 0.058 2647 Dihedral : 22.828 158.538 3180 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.77 % Allowed : 22.80 % Favored : 73.44 % 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: -3.29 (0.18), residues: 1773 helix: -1.09 (0.20), residues: 556 sheet: -3.22 (0.29), residues: 245 loop : -2.62 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 829 HIS 0.007 0.001 HIS B 313 PHE 0.021 0.002 PHE A 916 TYR 0.018 0.002 TYR D 68 ARG 0.014 0.001 ARG A 972 *********************** 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 324 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 265 time to evaluate : 1.917 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: A 773 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6731 (ttt180) REVERT: A 844 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5947 (mtpt) REVERT: A 858 MET cc_start: 0.7555 (mmt) cc_final: 0.7098 (mmp) REVERT: A 984 MET cc_start: 0.6817 (mmt) cc_final: 0.6516 (mmt) REVERT: A 994 TYR cc_start: 0.8128 (t80) cc_final: 0.7291 (t80) REVERT: B 172 TRP cc_start: 0.7940 (t-100) cc_final: 0.7328 (t-100) REVERT: B 196 ILE cc_start: 0.6482 (tp) cc_final: 0.6269 (tp) REVERT: C 466 VAL cc_start: 0.8170 (t) cc_final: 0.7643 (p) REVERT: C 470 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7535 (mp) REVERT: C 841 MET cc_start: 0.4570 (mmp) cc_final: 0.4086 (mmp) REVERT: C 842 ASN cc_start: 0.7876 (m-40) cc_final: 0.7570 (m-40) REVERT: C 849 MET cc_start: 0.6002 (tpt) cc_final: 0.5765 (tpp) REVERT: D 206 PHE cc_start: 0.7015 (m-80) cc_final: 0.6753 (m-80) outliers start: 59 outliers final: 38 residues processed: 309 average time/residue: 0.2752 time to fit residues: 129.5711 Evaluate side-chains 264 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE 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: 1.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17156 Z= 0.229 Angle : 0.682 10.100 23682 Z= 0.358 Chirality : 0.043 0.215 2589 Planarity : 0.005 0.056 2647 Dihedral : 22.807 158.759 3180 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.83 % Allowed : 24.07 % Favored : 72.09 % 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: -3.05 (0.19), residues: 1773 helix: -0.86 (0.21), residues: 552 sheet: -3.07 (0.28), residues: 261 loop : -2.47 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 829 HIS 0.006 0.001 HIS A 990 PHE 0.028 0.002 PHE C 698 TYR 0.019 0.002 TYR C 707 ARG 0.011 0.001 ARG A 972 *********************** 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 307 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.7202 (mmt) cc_final: 0.6999 (tpp) REVERT: A 773 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6662 (ttt180) REVERT: A 844 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5990 (mtpt) REVERT: A 916 PHE cc_start: 0.7442 (t80) cc_final: 0.7188 (t80) REVERT: B 172 TRP cc_start: 0.7931 (t-100) cc_final: 0.7277 (t-100) REVERT: C 466 VAL cc_start: 0.8073 (t) cc_final: 0.7819 (p) REVERT: C 605 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 788 VAL cc_start: 0.7879 (t) cc_final: 0.6634 (t) REVERT: C 842 ASN cc_start: 0.7822 (m-40) cc_final: 0.7501 (m-40) outliers start: 60 outliers final: 44 residues processed: 292 average time/residue: 0.2723 time to fit residues: 121.8430 Evaluate side-chains 262 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE 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: 5.9990 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 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: 0.7121 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17156 Z= 0.303 Angle : 0.712 10.005 23682 Z= 0.375 Chirality : 0.044 0.240 2589 Planarity : 0.005 0.073 2647 Dihedral : 22.899 158.480 3180 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 4.15 % Allowed : 23.88 % Favored : 71.97 % 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: -0.81 (0.21), residues: 551 sheet: -3.11 (0.29), residues: 268 loop : -2.44 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 829 HIS 0.006 0.001 HIS B 94 PHE 0.027 0.002 PHE D 48 TYR 0.018 0.002 TYR D 68 ARG 0.010 0.001 ARG A 972 *********************** 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 291 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 226 time to evaluate : 1.824 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: A 916 PHE cc_start: 0.7510 (t80) cc_final: 0.7275 (t80) REVERT: C 466 VAL cc_start: 0.8276 (t) cc_final: 0.7851 (p) REVERT: C 605 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (p) REVERT: C 788 VAL cc_start: 0.7931 (t) cc_final: 0.6729 (t) REVERT: C 841 MET cc_start: 0.4479 (mmp) cc_final: 0.4232 (mmp) REVERT: C 842 ASN cc_start: 0.7815 (m-40) cc_final: 0.7521 (m-40) outliers start: 65 outliers final: 47 residues processed: 275 average time/residue: 0.2972 time to fit residues: 124.9992 Evaluate side-chains 256 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8924 ------------------------------------------------------------------------------- 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 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 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17156 Z= 0.222 Angle : 0.699 15.581 23682 Z= 0.364 Chirality : 0.043 0.227 2589 Planarity : 0.005 0.056 2647 Dihedral : 22.871 158.607 3180 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.19 % Allowed : 25.35 % Favored : 71.46 % 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: -0.73 (0.21), residues: 551 sheet: -3.03 (0.28), residues: 275 loop : -2.37 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 956 HIS 0.008 0.001 HIS B 94 PHE 0.019 0.002 PHE A 916 TYR 0.016 0.002 TYR B 91 ARG 0.011 0.001 ARG A 972 *********************** 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 298 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 TYR cc_start: 0.7614 (t80) cc_final: 0.7405 (t80) REVERT: A 568 MET cc_start: 0.5884 (tpt) cc_final: 0.5458 (tpt) REVERT: A 773 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6788 (ttt180) REVERT: B 172 TRP cc_start: 0.7905 (t-100) cc_final: 0.7543 (t-100) REVERT: B 213 ASN cc_start: 0.8031 (t0) cc_final: 0.7800 (t0) REVERT: C 466 VAL cc_start: 0.8169 (t) cc_final: 0.7818 (p) REVERT: C 605 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (p) REVERT: C 785 ILE cc_start: 0.7833 (mp) cc_final: 0.7536 (mt) REVERT: C 788 VAL cc_start: 0.7780 (t) cc_final: 0.7032 (t) REVERT: C 842 ASN cc_start: 0.7720 (m-40) cc_final: 0.7422 (m-40) REVERT: C 858 MET cc_start: 0.6605 (mmp) cc_final: 0.6324 (mmp) REVERT: C 883 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6814 (tpp) outliers start: 50 outliers final: 33 residues processed: 285 average time/residue: 0.2761 time to fit residues: 119.2790 Evaluate side-chains 244 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 0.0020 chunk 157 optimal weight: 6.9990 chunk 167 optimal weight: 0.3980 chunk 101 optimal weight: 0.0870 chunk 73 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.2968 ------------------------------------------------------------------------------- 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 16 GLN ** 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 C 800 ASN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4409 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= 0.241 Angle : 0.713 17.857 23682 Z= 0.369 Chirality : 0.043 0.186 2589 Planarity : 0.005 0.071 2647 Dihedral : 22.852 158.736 3180 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.00 % Allowed : 25.67 % Favored : 71.33 % 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: -2.83 (0.19), residues: 1773 helix: -0.61 (0.22), residues: 551 sheet: -2.88 (0.28), residues: 275 loop : -2.38 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 956 HIS 0.008 0.001 HIS B 94 PHE 0.027 0.002 PHE A 916 TYR 0.019 0.002 TYR C 481 ARG 0.011 0.001 ARG C 703 *********************** 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 266 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 219 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLU cc_start: 0.6207 (tt0) cc_final: 0.5823 (mt-10) REVERT: A 658 MET cc_start: 0.7728 (mpp) cc_final: 0.6772 (ptp) REVERT: A 773 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6787 (ttt180) REVERT: A 994 TYR cc_start: 0.8027 (t80) cc_final: 0.7393 (t80) REVERT: B 172 TRP cc_start: 0.7907 (t-100) cc_final: 0.7547 (t-100) REVERT: B 215 THR cc_start: 0.7686 (t) cc_final: 0.7401 (p) REVERT: C 466 VAL cc_start: 0.8169 (t) cc_final: 0.7774 (p) REVERT: C 785 ILE cc_start: 0.7825 (mp) cc_final: 0.7366 (mt) REVERT: C 788 VAL cc_start: 0.7591 (t) cc_final: 0.6932 (t) REVERT: C 883 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6943 (tpp) outliers start: 47 outliers final: 38 residues processed: 258 average time/residue: 0.2872 time to fit residues: 113.4661 Evaluate side-chains 251 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 832 THR Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE 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: 2.9990 chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 chunk 15 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17156 Z= 0.222 Angle : 0.714 13.285 23682 Z= 0.369 Chirality : 0.043 0.185 2589 Planarity : 0.005 0.056 2647 Dihedral : 22.841 158.833 3180 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 2.87 % Allowed : 25.93 % Favored : 71.20 % 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: -2.81 (0.19), residues: 1773 helix: -0.54 (0.22), residues: 551 sheet: -2.88 (0.27), residues: 299 loop : -2.36 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 956 HIS 0.009 0.001 HIS B 94 PHE 0.021 0.002 PHE D 206 TYR 0.018 0.002 TYR C 481 ARG 0.007 0.001 ARG C 915 ********************** 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 279 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 658 MET cc_start: 0.7705 (mpp) cc_final: 0.7281 (ptp) REVERT: A 773 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6884 (ttt180) REVERT: B 172 TRP cc_start: 0.7811 (t-100) cc_final: 0.7506 (t-100) REVERT: B 213 ASN cc_start: 0.8192 (t0) cc_final: 0.7883 (t0) REVERT: B 215 THR cc_start: 0.7633 (t) cc_final: 0.7330 (p) REVERT: C 466 VAL cc_start: 0.8085 (t) cc_final: 0.7728 (p) REVERT: C 711 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 785 ILE cc_start: 0.7855 (mp) cc_final: 0.7371 (mt) REVERT: C 788 VAL cc_start: 0.7535 (t) cc_final: 0.7034 (t) REVERT: C 848 MET cc_start: 0.6666 (mmm) cc_final: 0.6169 (mmt) REVERT: C 883 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6919 (tpp) outliers start: 45 outliers final: 42 residues processed: 271 average time/residue: 0.2690 time to fit residues: 112.1724 Evaluate side-chains 263 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 773 ARG Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 599 CYS Chi-restraints excluded: chain C residue 678 GLU Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 832 THR Chi-restraints excluded: chain C residue 883 MET Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** 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 = 0.4151 r_free = 0.4151 target = 0.144088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.130652 restraints weight = 35043.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132737 restraints weight = 22656.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134224 restraints weight = 16375.617| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17156 Z= 0.217 Angle : 0.723 14.960 23682 Z= 0.375 Chirality : 0.043 0.161 2589 Planarity : 0.005 0.083 2647 Dihedral : 22.826 158.925 3180 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.94 % Allowed : 25.99 % Favored : 71.07 % 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: -2.73 (0.19), residues: 1773 helix: -0.45 (0.22), residues: 554 sheet: -2.79 (0.27), residues: 299 loop : -2.36 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 829 HIS 0.008 0.001 HIS B 94 PHE 0.020 0.002 PHE D 206 TYR 0.019 0.002 TYR C 481 ARG 0.008 0.001 ARG C 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.37 seconds wall clock time: 61 minutes 25.64 seconds (3685.64 seconds total)