Starting phenix.real_space_refine on Sun Feb 18 19:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9c_24256/02_2024/7n9c_24256.pdb" } resolution = 3.71 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= 0.004 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 14499 2.51 5 N 3826 2.21 5 O 4311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 678": "OD1" <-> "OD2" Residue "A PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 837": "OD1" <-> "OD2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A ASP 888": "OD1" <-> "OD2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A TYR 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1042": "OD1" <-> "OD2" Residue "A ASP 1071": "OD1" <-> "OD2" Residue "A PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 746": "OE1" <-> "OE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B ASP 755": "OD1" <-> "OD2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B GLU 872": "OE1" <-> "OE2" Residue "B ASP 900": "OD1" <-> "OD2" Residue "B GLU 960": "OE1" <-> "OE2" Residue "B PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1042": "OD1" <-> "OD2" Residue "B ASP 1086": "OD1" <-> "OD2" Residue "B TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1109": "OE1" <-> "OE2" Residue "B GLU 1123": "OE1" <-> "OE2" Residue "B PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1236": "OE1" <-> "OE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 794": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C GLU 872": "OE1" <-> "OE2" Residue "C TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22734 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7542 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 54, 'TRANS': 925} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 6220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6220 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 46, 'TRANS': 765} Chain breaks: 7 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 7018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7018 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 53, 'TRANS': 921} Chain breaks: 7 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 798 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 10, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 370 Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 12.10, per 1000 atoms: 0.53 Number of scatterers: 22734 At special positions: 0 Unit cell: (136.74, 140.98, 182.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4311 8.00 N 3826 7.00 C 14499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 258 " distance=2.05 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 763 " distance=2.02 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 852 " distance=2.02 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS A1124 " - pdb=" SG CYS A1135 " distance=2.01 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS A1218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 258 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 393 " distance=2.02 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 852 " distance=2.02 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 841 " distance=2.00 Simple disulfide: pdb=" SG CYS B1124 " - pdb=" SG CYS B1135 " distance=2.01 Simple disulfide: pdb=" SG CYS B1174 " - pdb=" SG CYS B1218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 223 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 428 " - pdb=" SG CYS C 453 " distance=2.01 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 524 " distance=1.99 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 682 " distance=2.02 Simple disulfide: pdb=" SG CYS C 709 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 754 " - pdb=" SG CYS C 763 " distance=2.02 Simple disulfide: pdb=" SG CYS C 830 " - pdb=" SG CYS C 852 " distance=2.01 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 841 " distance=2.02 Simple disulfide: pdb=" SG CYS C1124 " - pdb=" SG CYS C1135 " distance=2.01 Simple disulfide: pdb=" SG CYS C1174 " - pdb=" SG CYS C1218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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: 9.94 Conformation dependent library (CDL) restraints added in 4.2 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5644 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 48 sheets defined 26.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 457 through 463 removed outlier: 4.065A pdb=" N TYR A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.583A pdb=" N LEU A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 480 " --> pdb=" O THR A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 495 through 502 removed outlier: 4.964A pdb=" N ARG A 500 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.921A pdb=" N ASP A 512 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.573A pdb=" N GLN A 598 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.644A pdb=" N SER A 729 " --> pdb=" O ARG A 726 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 730 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 836 Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.883A pdb=" N GLN A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 874 removed outlier: 3.700A pdb=" N ASP A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 870 " --> pdb=" O GLN A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 916 Processing helix chain 'A' and resid 958 through 977 removed outlier: 3.604A pdb=" N GLY A 977 " --> pdb=" O THR A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.598A pdb=" N GLY A 981 " --> pdb=" O TRP A 978 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 982 " --> pdb=" O THR A 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 978 through 982' Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.733A pdb=" N TYR A 996 " --> pdb=" O MET A 992 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 4.249A pdb=" N LEU A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1033 removed outlier: 3.681A pdb=" N GLN A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1049 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1058 through 1060 No H-bonds generated for 'chain 'A' and resid 1058 through 1060' Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1077 through 1125 removed outlier: 4.535A pdb=" N VAL A1083 " --> pdb=" O PRO A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 829 through 836 Processing helix chain 'B' and resid 838 through 847 removed outlier: 3.641A pdb=" N SER B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 875 removed outlier: 3.767A pdb=" N ASP B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 870 " --> pdb=" O GLN B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 918 Processing helix chain 'B' and resid 958 through 977 Processing helix chain 'B' and resid 978 through 983 removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O TRP B 978 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 983 " --> pdb=" O PHE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1001 Processing helix chain 'B' and resid 1005 through 1011 removed outlier: 3.710A pdb=" N TYR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1033 removed outlier: 3.815A pdb=" N GLN B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1049 Processing helix chain 'B' and resid 1051 through 1058 Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1077 through 1125 removed outlier: 4.443A pdb=" N VAL B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B1108 " --> pdb=" O LEU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1240 removed outlier: 4.165A pdb=" N GLU B1236 " --> pdb=" O PRO B1232 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.903A pdb=" N VAL C 433 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.574A pdb=" N ALA C 444 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 445' Processing helix chain 'C' and resid 456 through 462 removed outlier: 3.911A pdb=" N LEU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.379A pdb=" N ASN C 480 " --> pdb=" O THR C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 530 through 535 Processing helix chain 'C' and resid 594 through 598 Processing helix chain 'C' and resid 711 through 716 Processing helix chain 'C' and resid 722 through 730 removed outlier: 4.584A pdb=" N TYR C 728 " --> pdb=" O THR C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 835 Processing helix chain 'C' and resid 839 through 846 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 850 through 875 removed outlier: 3.533A pdb=" N ASP C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 870 " --> pdb=" O GLN C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 918 Processing helix chain 'C' and resid 958 through 977 Processing helix chain 'C' and resid 989 through 1001 Processing helix chain 'C' and resid 1005 through 1010 Processing helix chain 'C' and resid 1011 through 1032 removed outlier: 3.582A pdb=" N ILE C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C1028 " --> pdb=" O GLY C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1036 removed outlier: 3.775A pdb=" N ALA C1036 " --> pdb=" O THR C1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1033 through 1036' Processing helix chain 'C' and resid 1037 through 1057 removed outlier: 3.723A pdb=" N VAL C1043 " --> pdb=" O LYS C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1060 No H-bonds generated for 'chain 'C' and resid 1058 through 1060' Processing helix chain 'C' and resid 1068 through 1075 Processing helix chain 'C' and resid 1077 through 1125 removed outlier: 4.923A pdb=" N VAL C1083 " --> pdb=" O PRO C1079 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN C1084 " --> pdb=" O GLU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1239 removed outlier: 3.551A pdb=" N GLU C1236 " --> pdb=" O PRO C1232 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.916A pdb=" N LYS E 65 " --> pdb=" O ASN E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.281A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.559A pdb=" N THR A 121 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN A 153 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 361 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER A 297 " --> pdb=" O PRO A 317 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N HIS A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N LEU A 315 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 128 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.080A pdb=" N ALA C 667 " --> pdb=" O GLY C 658 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 666 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 144 removed outlier: 3.550A pdb=" N ASP A 379 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177 removed outlier: 3.532A pdb=" N LEU A 176 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 411 removed outlier: 6.737A pdb=" N VAL A 687 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 409 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 685 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY A 686 " --> pdb=" O GLN A 705 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 446 through 450 removed outlier: 3.546A pdb=" N VAL A 604 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 600 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 523 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 470 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR E 104 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 removed outlier: 6.227A pdb=" N CYS A 453 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 658 removed outlier: 6.556A pdb=" N PHE A 657 " --> pdb=" O PHE B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 746 through 747 removed outlier: 6.384A pdb=" N ILE A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AB4, first strand: chain 'A' and resid 803 through 820 removed outlier: 6.157A pdb=" N GLN A1163 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 810 " --> pdb=" O PRO A1161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 812 " --> pdb=" O TYR A1159 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A1159 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 814 " --> pdb=" O VAL A1157 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1157 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 816 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A1155 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 818 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1153 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A1151 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER A1147 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A1153 " --> pdb=" O PRO A1145 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A1155 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1143 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A1157 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 803 through 820 removed outlier: 6.157A pdb=" N GLN A1163 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 810 " --> pdb=" O PRO A1161 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 812 " --> pdb=" O TYR A1159 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR A1159 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 814 " --> pdb=" O VAL A1157 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1157 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 816 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A1155 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 818 " --> pdb=" O VAL A1153 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1153 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A1151 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1168 " --> pdb=" O SER A1189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 828 Processing sheet with id=AB7, first strand: chain 'A' and resid 1212 through 1214 Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.596A pdb=" N SER B 152 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASN B 153 " --> pdb=" O TYR B 361 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR B 361 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER B 297 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N HIS B 299 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LEU B 315 " --> pdb=" O HIS B 299 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 128 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 140 through 147 removed outlier: 3.591A pdb=" N ASP B 145 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 379 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 176 through 177 removed outlier: 3.747A pdb=" N GLY B 195 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 403 through 411 removed outlier: 6.960A pdb=" N VAL B 687 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN B 409 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 685 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 686 " --> pdb=" O GLN B 705 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 417 through 419 removed outlier: 6.859A pdb=" N ILE B 418 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 666 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY B 658 " --> pdb=" O ASP B 666 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 657 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 746 through 747 removed outlier: 6.405A pdb=" N ILE B 762 " --> pdb=" O ILE B 758 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AC6, first strand: chain 'B' and resid 806 through 807 Processing sheet with id=AC7, first strand: chain 'B' and resid 810 through 820 removed outlier: 5.722A pdb=" N TYR B1159 " --> pdb=" O HIS B1140 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS B1140 " --> pdb=" O TYR B1159 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 825 through 828 removed outlier: 4.392A pdb=" N LYS B 825 " --> pdb=" O LEU B 953 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1168 through 1169 removed outlier: 3.889A pdb=" N THR B1168 " --> pdb=" O SER B1189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1212 through 1214 Processing sheet with id=AD2, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AD3, first strand: chain 'C' and resid 139 through 147 removed outlier: 3.598A pdb=" N ASP C 145 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR C 366 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP C 382 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 368 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS C 370 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.535A pdb=" N LYS C 221 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 316 through 321 removed outlier: 7.089A pdb=" N ILE C 295 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP C 320 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE C 293 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 280 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU C 188 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 282 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 182 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 403 through 411 removed outlier: 5.663A pdb=" N ILE C 404 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR C 691 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN C 406 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 689 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 408 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY C 686 " --> pdb=" O GLN C 705 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 446 through 450 removed outlier: 4.148A pdb=" N ASN C 446 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 491 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 494 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 601 " --> pdb=" O TRP C 528 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 605 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 524 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 removed outlier: 6.524A pdb=" N CYS C 453 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 544 through 546 Processing sheet with id=AE1, first strand: chain 'C' and resid 746 through 747 removed outlier: 6.886A pdb=" N GLU C 746 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N THR C 788 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 803 through 820 removed outlier: 6.651A pdb=" N SER C 803 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1168 " --> pdb=" O SER C 803 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 805 " --> pdb=" O ASN C1166 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN C1166 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C1164 " --> pdb=" O PRO C 807 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C1151 " --> pdb=" O ALA C1148 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C1148 " --> pdb=" O GLY C1151 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C1159 " --> pdb=" O HIS C1140 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N HIS C1140 " --> pdb=" O TYR C1159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 803 through 820 removed outlier: 6.651A pdb=" N SER C 803 " --> pdb=" O THR C1168 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1168 " --> pdb=" O SER C 803 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 805 " --> pdb=" O ASN C1166 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN C1166 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C1164 " --> pdb=" O PRO C 807 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C1168 " --> pdb=" O SER C1189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C1170 " --> pdb=" O PHE C1187 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE C1187 " --> pdb=" O ALA C1170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 826 through 828 Processing sheet with id=AE5, first strand: chain 'C' and resid 1212 through 1217 removed outlier: 4.013A pdb=" N ALA C1179 " --> pdb=" O SER C1215 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.584A pdb=" N TYR D 59 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 97 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.584A pdb=" N TYR D 59 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 97 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 68 through 72 removed outlier: 3.882A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.521A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR E 115 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.521A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 39 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 70 through 73 removed outlier: 3.679A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2634 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.42 Time building geometry restraints manager: 10.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 1850 1.24 - 1.38: 6917 1.38 - 1.53: 12315 1.53 - 1.67: 2029 1.67 - 1.82: 126 Bond restraints: 23237 Sorted by residual: bond pdb=" C GLY C 496 " pdb=" O GLY C 496 " ideal model delta sigma weight residual 1.234 1.091 0.142 1.21e-02 6.83e+03 1.38e+02 bond pdb=" C TYR D 106 " pdb=" O TYR D 106 " ideal model delta sigma weight residual 1.234 1.108 0.126 1.26e-02 6.30e+03 9.94e+01 bond pdb=" C PHE A 469 " pdb=" O PHE A 469 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.22e-02 6.72e+03 8.81e+01 bond pdb=" C PHE C 469 " pdb=" O PHE C 469 " ideal model delta sigma weight residual 1.235 1.150 0.085 1.22e-02 6.72e+03 4.87e+01 bond pdb=" C VAL C 474 " pdb=" O VAL C 474 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.00e-02 1.00e+04 3.35e+01 ... (remaining 23232 not shown) Histogram of bond angle deviations from ideal: 85.56 - 97.91: 2 97.91 - 110.25: 5880 110.25 - 122.59: 22220 122.59 - 134.94: 3604 134.94 - 147.28: 1 Bond angle restraints: 31707 Sorted by residual: angle pdb=" CE2 TYR D 104 " pdb=" CZ TYR D 104 " pdb=" OH TYR D 104 " ideal model delta sigma weight residual 119.90 85.56 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N LEU A1051 " pdb=" CA LEU A1051 " pdb=" C LEU A1051 " ideal model delta sigma weight residual 113.97 101.58 12.39 1.28e+00 6.10e-01 9.37e+01 angle pdb=" C PRO C 476 " pdb=" CA PRO C 476 " pdb=" CB PRO C 476 " ideal model delta sigma weight residual 110.27 98.41 11.86 1.29e+00 6.01e-01 8.45e+01 angle pdb=" CE1 TYR D 104 " pdb=" CZ TYR D 104 " pdb=" OH TYR D 104 " ideal model delta sigma weight residual 119.90 147.28 -27.38 3.00e+00 1.11e-01 8.33e+01 angle pdb=" N LEU B1051 " pdb=" CA LEU B1051 " pdb=" C LEU B1051 " ideal model delta sigma weight residual 113.50 102.31 11.19 1.23e+00 6.61e-01 8.28e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12588 17.95 - 35.90: 1019 35.90 - 53.84: 135 53.84 - 71.79: 45 71.79 - 89.74: 33 Dihedral angle restraints: 13820 sinusoidal: 5063 harmonic: 8757 Sorted by residual: dihedral pdb=" CB CYS A 383 " pdb=" SG CYS A 383 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual -86.00 -173.36 87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C 383 " pdb=" SG CYS C 383 " pdb=" SG CYS C 393 " pdb=" CB CYS C 393 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" C PHE C 469 " pdb=" N PHE C 469 " pdb=" CA PHE C 469 " pdb=" CB PHE C 469 " ideal model delta harmonic sigma weight residual -122.60 -143.51 20.91 0 2.50e+00 1.60e-01 7.00e+01 ... (remaining 13817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 3101 0.157 - 0.314: 560 0.314 - 0.471: 8 0.471 - 0.628: 0 0.628 - 0.785: 1 Chirality restraints: 3670 Sorted by residual: chirality pdb=" CA PHE C 469 " pdb=" N PHE C 469 " pdb=" C PHE C 469 " pdb=" CB PHE C 469 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA GLN B1234 " pdb=" N GLN B1234 " pdb=" C GLN B1234 " pdb=" CB GLN B1234 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA TYR D 103 " pdb=" N TYR D 103 " pdb=" C TYR D 103 " pdb=" CB TYR D 103 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 3667 not shown) Planarity restraints: 4133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 104 " -0.011 2.00e-02 2.50e+03 8.74e-02 1.53e+02 pdb=" CG TYR D 104 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR D 104 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 104 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR D 104 " 0.126 2.00e-02 2.50e+03 pdb=" CE2 TYR D 104 " 0.101 2.00e-02 2.50e+03 pdb=" CZ TYR D 104 " -0.169 2.00e-02 2.50e+03 pdb=" OH TYR D 104 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 474 " -0.028 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C VAL C 474 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL C 474 " -0.039 2.00e-02 2.50e+03 pdb=" N SER C 475 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 109 " -0.000 2.00e-02 2.50e+03 3.67e-02 2.36e+01 pdb=" CG PHE E 109 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE E 109 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 109 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE E 109 " 0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE E 109 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 109 " -0.058 2.00e-02 2.50e+03 ... (remaining 4130 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1948 2.73 - 3.27: 22984 3.27 - 3.81: 35970 3.81 - 4.36: 45872 4.36 - 4.90: 76148 Nonbonded interactions: 182922 Sorted by model distance: nonbonded pdb=" O PHE C 466 " pdb=" OH TYR D 59 " model vdw 2.185 2.440 nonbonded pdb=" O ALA A 464 " pdb=" OH TYR E 59 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR A 461 " pdb=" O PRO A 476 " model vdw 2.229 2.440 nonbonded pdb=" O SER C 976 " pdb=" OG1 THR C 979 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR B 848 " pdb=" OD2 ASP B1086 " model vdw 2.283 2.440 ... (remaining 182917 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 119 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 158 or resid 174 through 178 o \ r (resid 179 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 80 through 185 or (resid 186 through 192 and (name N or name CA or name C or nam \ e O or name CB )) or resid 193 through 199 or (resid 200 through 208 and (name N \ or name CA or name C or name O or name CB )) or resid 209 through 211 or (resid \ 212 and (name N or name CA or name C or name O or name CB )) or resid 213 throu \ gh 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or \ resid 219 through 225 or (resid 226 and (name N or name CA or name C or name O \ or name CB )) or resid 227 through 229 or (resid 230 and (name N or name CA or n \ ame C or name O or name CB )) or resid 231 or (resid 232 and (name N or name CA \ or name C or name O or name CB )) or resid 258 or (resid 259 through 282 and (na \ me N or name CA or name C or name O or name CB )) or resid 283 through 289 or (r \ esid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 296 or (resid 297 and (name N or name CA or name C or name O or name CB ) \ ) or resid 298 through 299 or (resid 300 and (name N or name CA or name C or nam \ e O or name CB )) or resid 301 through 309 or (resid 310 and (name N or name CA \ or name C or name O or name CB )) or resid 311 through 320 or (resid 321 and (na \ me N or name CA or name C or name O or name CB )) or resid 322 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 t \ hrough 415 or (resid 416 and (name N or name CA or name C or name O or name CB ) \ ) or resid 417 through 423 or (resid 424 through 427 and (name N or name CA or n \ ame C or name O or name CB )) or resid 428 through 431 or (resid 432 through 434 \ and (name N or name CA or name C or name O or name CB )) or resid 435 through 4 \ 36 or (resid 437 through 438 and (name N or name CA or name C or name O or name \ CB )) or resid 439 through 440 or (resid 441 through 444 and (name N or name CA \ or name C or name O or name CB )) or resid 445 through 448 or (resid 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 thr \ ough 452 and (name N or name CA or name C or name O or name CB )) or resid 453 t \ hrough 455 or (resid 456 through 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 or (resid 467 through 470 and (name N or name CA or n \ ame C or name O or name CB )) or resid 471 or (resid 472 and (name N or name CA \ or name C or name O or name CB )) or resid 473 or (resid 474 through 475 and (na \ me N or name CA or name C or name O or name CB )) or resid 476 or (resid 477 thr \ ough 482 and (name N or name CA or name C or name O or name CB )) or resid 483 t \ hrough 489 or (resid 490 through 495 and (name N or name CA or name C or name O \ or name CB )) or resid 496 or (resid 497 through 503 and (name N or name CA or n \ ame C or name O or name CB )) or resid 504 through 505 or (resid 506 through 507 \ and (name N or name CA or name C or name O or name CB )) or resid 508 or (resid \ 509 through 517 and (name N or name CA or name C or name O or name CB )) or res \ id 518 or (resid 519 through 522 and (name N or name CA or name C or name O or n \ ame CB )) or resid 523 through 524 or (resid 525 through 529 and (name N or name \ CA or name C or name O or name CB )) or resid 530 through 533 or (resid 534 thr \ ough 537 and (name N or name CA or name C or name O or name CB )) or resid 538 t \ hrough 539 or (resid 540 through 587 and (name N or name CA or name C or name O \ or name CB )) or resid 588 or (resid 589 through 590 and (name N or name CA or n \ ame C or name O or name CB )) or resid 591 or (resid 592 through 593 and (name N \ or name CA or name C or name O or name CB )) or resid 594 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throu \ gh 599 or (resid 600 through 612 and (name N or name CA or name C or name O or n \ ame CB )) or resid 613 through 614 or (resid 615 through 616 and (name N or name \ CA or name C or name O or name CB )) or resid 617 through 619 or (resid 620 thr \ ough 623 and (name N or name CA or name C or name O or name CB )) or resid 624 t \ hrough 628 or (resid 629 and (name N or name CA or name C or name O or name CB ) \ ) or resid 630 through 672 or (resid 673 and (name N or name CA or name C or nam \ e O or name CB )) or resid 674 through 745 or (resid 746 and (name N or name CA \ or name C or name O or name CB )) or resid 747 through 836 or (resid 837 through \ 838 and (name N or name CA or name C or name O or name CB )) or resid 839 or (r \ esid 840 and (name N or name CA or name C or name O or name CB )) or resid 841 o \ r (resid 842 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 43 through 849 or (resid 850 and (name N or name CA or name C or name O or name \ CB )) or resid 851 through 902 or (resid 903 and (name N or name CA or name C or \ name O or name CB )) or resid 904 through 905 or (resid 906 and (name N or name \ CA or name C or name O or name CB )) or resid 907 through 919 or resid 948 thro \ ugh 1028 or (resid 1029 and (name N or name CA or name C or name O or name CB )) \ or resid 1030 or (resid 1031 through 1033 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1034 through 1065 or (resid 1066 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1067 through 1079 or (resid 1080 \ through 1081 and (name N or name CA or name C or name O or name CB )) or resid \ 1082 through 1218 or (resid 1219 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1220 through 1233 or (resid 1234 and (name N or name CA or na \ me C or name O or name CB )) or resid 1235 through 1239)) selection = (chain 'C' and (resid 119 through 232 or resid 258 through 264 or (resid 279 thr \ ough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 t \ hrough 312 or (resid 313 through 314 and (name N or name CA or name C or name O \ or name CB )) or resid 315 through 319 or (resid 320 through 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 328 or (resid 329 \ and (name N or name CA or name C or name O or name CB )) or resid 330 through 5 \ 47 or resid 584 through 645 or (resid 646 and (name N or name CA or name C or na \ me O or name CB )) or resid 647 through 659 or (resid 660 and (name N or name CA \ or name C or name O or name CB )) or resid 661 through 767 or (resid 768 and (n \ ame N or name CA or name C or name O or name CB )) or resid 782 through 793 or ( \ resid 794 and (name N or name CA or name C or name O or name CB )) or resid 795 \ through 885 or (resid 886 and (name N or name CA or name C or name O or name CB \ )) or resid 887 through 904 or (resid 905 through 906 and (name N or name CA or \ name C or name O or name CB )) or resid 907 through 1238 or (resid 1239 and (nam \ e N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and (resid 1 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 126)) selection = (chain 'E' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 126)) } 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.770 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 63.260 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.142 23237 Z= 0.875 Angle : 1.629 34.337 31707 Z= 1.175 Chirality : 0.112 0.785 3670 Planarity : 0.009 0.087 4133 Dihedral : 13.879 89.738 8071 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.21 % Allowed : 4.40 % Favored : 95.39 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2967 helix: 1.40 (0.20), residues: 657 sheet: -0.32 (0.20), residues: 631 loop : -1.39 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 528 HIS 0.007 0.002 HIS A 611 PHE 0.061 0.003 PHE E 109 TYR 0.169 0.005 TYR D 104 ARG 0.010 0.001 ARG C 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 239 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6588 (p0) REVERT: B 306 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7384 (mtp-110) REVERT: B 1062 PHE cc_start: 0.8363 (m-80) cc_final: 0.8105 (m-80) REVERT: B 1214 VAL cc_start: 0.8826 (t) cc_final: 0.8555 (m) REVERT: C 331 GLN cc_start: 0.6543 (mm110) cc_final: 0.6282 (tp40) REVERT: C 423 ASN cc_start: 0.5366 (t0) cc_final: 0.4924 (p0) REVERT: C 466 PHE cc_start: 0.2446 (t80) cc_final: 0.2175 (t80) REVERT: C 834 ILE cc_start: 0.9286 (mt) cc_final: 0.8985 (mt) REVERT: E 34 MET cc_start: 0.3956 (ppp) cc_final: 0.3293 (ppp) outliers start: 5 outliers final: 0 residues processed: 243 average time/residue: 0.3273 time to fit residues: 130.4615 Evaluate side-chains 180 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 876 GLN A 879 GLN A1041 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23237 Z= 0.178 Angle : 0.582 9.189 31707 Z= 0.313 Chirality : 0.045 0.317 3670 Planarity : 0.005 0.053 4133 Dihedral : 5.056 56.729 3203 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.96 % Allowed : 8.52 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2967 helix: 1.46 (0.20), residues: 664 sheet: -0.44 (0.19), residues: 700 loop : -1.26 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 156 HIS 0.003 0.001 HIS C 158 PHE 0.014 0.001 PHE A 284 TYR 0.022 0.001 TYR C1159 ARG 0.005 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 244 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 ASN cc_start: 0.6833 (OUTLIER) cc_final: 0.6247 (p0) REVERT: A 956 LEU cc_start: 0.8728 (tp) cc_final: 0.8411 (tt) REVERT: B 306 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7319 (mtp-110) REVERT: B 1043 VAL cc_start: 0.9030 (t) cc_final: 0.8527 (p) REVERT: B 1047 ASN cc_start: 0.8026 (m110) cc_final: 0.7560 (m110) REVERT: B 1057 GLN cc_start: 0.8012 (mm110) cc_final: 0.7509 (mm-40) REVERT: B 1062 PHE cc_start: 0.8144 (m-80) cc_final: 0.7226 (m-80) REVERT: C 156 TRP cc_start: 0.5842 (t60) cc_final: 0.5613 (t60) REVERT: C 423 ASN cc_start: 0.5481 (t0) cc_final: 0.4831 (p0) REVERT: C 666 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.7044 (p0) REVERT: C 865 GLU cc_start: 0.7545 (tt0) cc_final: 0.7246 (tt0) REVERT: D 20 LEU cc_start: 0.2694 (mt) cc_final: 0.2375 (mt) REVERT: D 50 THR cc_start: 0.2157 (OUTLIER) cc_final: 0.1610 (m) REVERT: E 34 MET cc_start: 0.4445 (ppp) cc_final: 0.3988 (ppp) outliers start: 23 outliers final: 12 residues processed: 259 average time/residue: 0.3170 time to fit residues: 133.6900 Evaluate side-chains 203 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 0.0020 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 243 optimal weight: 0.0060 chunk 270 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN B 288 ASN ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23237 Z= 0.164 Angle : 0.535 8.814 31707 Z= 0.283 Chirality : 0.044 0.179 3670 Planarity : 0.004 0.052 4133 Dihedral : 4.752 57.318 3203 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.47 % Allowed : 10.49 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2967 helix: 1.61 (0.21), residues: 650 sheet: -0.38 (0.19), residues: 739 loop : -1.26 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 156 HIS 0.002 0.000 HIS A 611 PHE 0.014 0.001 PHE E 47 TYR 0.027 0.001 TYR D 104 ARG 0.010 0.000 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 2.848 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 145 ASP cc_start: 0.7974 (m-30) cc_final: 0.7688 (m-30) REVERT: A 946 LYS cc_start: 0.5565 (tmtt) cc_final: 0.5361 (tptp) REVERT: A 956 LEU cc_start: 0.8805 (tp) cc_final: 0.8439 (tt) REVERT: A 1109 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: B 1043 VAL cc_start: 0.9019 (t) cc_final: 0.8728 (p) REVERT: B 1047 ASN cc_start: 0.7970 (m110) cc_final: 0.7680 (m110) REVERT: B 1057 GLN cc_start: 0.7972 (mm110) cc_final: 0.7431 (mm-40) REVERT: B 1062 PHE cc_start: 0.8034 (m-80) cc_final: 0.7036 (m-80) REVERT: B 1231 ASP cc_start: 0.7970 (t0) cc_final: 0.7513 (t70) REVERT: C 423 ASN cc_start: 0.5366 (t0) cc_final: 0.4744 (p0) REVERT: E 34 MET cc_start: 0.4406 (ppp) cc_final: 0.3887 (ppp) outliers start: 35 outliers final: 19 residues processed: 239 average time/residue: 0.3186 time to fit residues: 123.9288 Evaluate side-chains 206 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 3.9990 chunk 205 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 GLN B 288 ASN ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 23237 Z= 0.444 Angle : 0.691 12.622 31707 Z= 0.366 Chirality : 0.048 0.185 3670 Planarity : 0.005 0.061 4133 Dihedral : 5.371 32.756 3201 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.73 % Allowed : 13.42 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2967 helix: 0.81 (0.20), residues: 682 sheet: -0.70 (0.19), residues: 686 loop : -1.59 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 156 HIS 0.005 0.002 HIS B1150 PHE 0.031 0.002 PHE A 998 TYR 0.020 0.002 TYR B 371 ARG 0.008 0.001 ARG B1111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 179 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 ASN cc_start: 0.7273 (p0) cc_final: 0.6839 (p0) REVERT: A 638 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6276 (pt) REVERT: A 956 LEU cc_start: 0.8825 (tp) cc_final: 0.8448 (tt) REVERT: A 1109 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: A 1121 MET cc_start: 0.8514 (tpp) cc_final: 0.8313 (tpp) REVERT: A 1217 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7445 (p0) REVERT: B 306 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6765 (ttp-110) REVERT: B 1057 GLN cc_start: 0.8187 (mm110) cc_final: 0.7684 (mm-40) REVERT: B 1062 PHE cc_start: 0.8142 (m-80) cc_final: 0.7220 (m-80) REVERT: C 157 PHE cc_start: 0.6424 (m-80) cc_final: 0.6182 (m-80) REVERT: C 423 ASN cc_start: 0.5478 (t0) cc_final: 0.4584 (p0) REVERT: C 1093 LEU cc_start: 0.8942 (tp) cc_final: 0.8677 (tt) REVERT: D 50 THR cc_start: 0.1614 (OUTLIER) cc_final: 0.1135 (m) REVERT: E 34 MET cc_start: 0.4544 (ppp) cc_final: 0.4083 (ppp) outliers start: 65 outliers final: 44 residues processed: 229 average time/residue: 0.3073 time to fit residues: 117.0370 Evaluate side-chains 229 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 678 ASP Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 698 ASN Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 215 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 876 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 HIS ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23237 Z= 0.155 Angle : 0.524 9.789 31707 Z= 0.274 Chirality : 0.043 0.175 3670 Planarity : 0.004 0.053 4133 Dihedral : 4.661 22.785 3201 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.27 % Allowed : 13.93 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2967 helix: 1.52 (0.21), residues: 658 sheet: -0.52 (0.19), residues: 704 loop : -1.37 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 156 HIS 0.002 0.000 HIS C1180 PHE 0.017 0.001 PHE A 492 TYR 0.018 0.001 TYR C1159 ARG 0.007 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 212 time to evaluate : 2.722 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 621 LYS cc_start: 0.6072 (mmtt) cc_final: 0.5849 (mmmt) REVERT: A 956 LEU cc_start: 0.8795 (tp) cc_final: 0.8403 (tt) REVERT: A 1109 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: A 1121 MET cc_start: 0.8344 (tpp) cc_final: 0.7973 (tpp) REVERT: A 1217 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 287 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7684 (ttpt) REVERT: B 306 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6584 (ttp-110) REVERT: B 406 GLN cc_start: 0.8319 (tt0) cc_final: 0.7937 (tp-100) REVERT: B 1043 VAL cc_start: 0.9021 (t) cc_final: 0.8711 (p) REVERT: B 1047 ASN cc_start: 0.7916 (m110) cc_final: 0.7586 (m110) REVERT: B 1057 GLN cc_start: 0.7987 (mm110) cc_final: 0.7503 (mm-40) REVERT: B 1062 PHE cc_start: 0.8042 (m-80) cc_final: 0.7045 (m-80) REVERT: B 1231 ASP cc_start: 0.8071 (t0) cc_final: 0.7554 (t70) REVERT: C 156 TRP cc_start: 0.5839 (OUTLIER) cc_final: 0.4789 (m100) REVERT: C 423 ASN cc_start: 0.5427 (t0) cc_final: 0.4352 (p0) REVERT: C 666 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7127 (p0) REVERT: C 755 ASP cc_start: 0.7435 (p0) cc_final: 0.6849 (m-30) REVERT: E 34 MET cc_start: 0.4605 (ppp) cc_final: 0.4147 (ppp) outliers start: 54 outliers final: 26 residues processed: 255 average time/residue: 0.3039 time to fit residues: 126.6392 Evaluate side-chains 228 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 666 ASP Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 0.0370 chunk 24 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23237 Z= 0.371 Angle : 0.622 12.036 31707 Z= 0.327 Chirality : 0.046 0.180 3670 Planarity : 0.005 0.049 4133 Dihedral : 5.062 31.274 3201 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.19 % Allowed : 15.10 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2967 helix: 1.06 (0.20), residues: 676 sheet: -0.74 (0.19), residues: 676 loop : -1.54 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 196 HIS 0.005 0.001 HIS C1193 PHE 0.026 0.002 PHE A 178 TYR 0.018 0.002 TYR C1159 ARG 0.006 0.001 ARG B1111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 188 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6053 (mmtt) cc_final: 0.5507 (mptt) REVERT: A 657 PHE cc_start: 0.6233 (t80) cc_final: 0.6023 (t80) REVERT: A 677 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 956 LEU cc_start: 0.8862 (tp) cc_final: 0.8446 (tt) REVERT: A 1109 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: A 1121 MET cc_start: 0.8432 (tpp) cc_final: 0.8230 (tpp) REVERT: A 1217 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 306 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6465 (ttp-110) REVERT: B 1057 GLN cc_start: 0.8138 (mm110) cc_final: 0.7684 (mm-40) REVERT: B 1062 PHE cc_start: 0.8090 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1111 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7237 (ttm170) REVERT: B 1231 ASP cc_start: 0.8086 (t0) cc_final: 0.7362 (t0) REVERT: C 157 PHE cc_start: 0.6444 (m-80) cc_final: 0.6236 (m-80) REVERT: C 210 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7302 (pp) REVERT: C 1093 LEU cc_start: 0.8952 (tp) cc_final: 0.8727 (tt) REVERT: E 34 MET cc_start: 0.4729 (ppp) cc_final: 0.4299 (ppp) outliers start: 76 outliers final: 54 residues processed: 245 average time/residue: 0.3059 time to fit residues: 123.5250 Evaluate side-chains 242 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 HIS Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 866 GLN Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 698 ASN Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 10.0000 chunk 32 optimal weight: 0.0000 chunk 165 optimal weight: 0.7980 chunk 211 optimal weight: 50.0000 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23237 Z= 0.188 Angle : 0.536 10.715 31707 Z= 0.281 Chirality : 0.044 0.260 3670 Planarity : 0.004 0.049 4133 Dihedral : 4.746 24.665 3201 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.43 % Allowed : 16.07 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2967 helix: 1.37 (0.21), residues: 665 sheet: -0.60 (0.19), residues: 698 loop : -1.42 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 156 HIS 0.002 0.001 HIS C1193 PHE 0.021 0.001 PHE A 178 TYR 0.018 0.001 TYR C1159 ARG 0.008 0.000 ARG B1075 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.5974 (mmtt) cc_final: 0.5471 (mptt) REVERT: A 956 LEU cc_start: 0.8782 (tp) cc_final: 0.8412 (tt) REVERT: A 1109 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: A 1121 MET cc_start: 0.8332 (tpp) cc_final: 0.7956 (tpp) REVERT: A 1217 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7460 (p0) REVERT: B 287 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7765 (ttpt) REVERT: B 306 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6571 (ttp-110) REVERT: B 1057 GLN cc_start: 0.8026 (mm110) cc_final: 0.7545 (mm-40) REVERT: B 1062 PHE cc_start: 0.8063 (m-80) cc_final: 0.7058 (m-80) REVERT: B 1231 ASP cc_start: 0.8001 (t0) cc_final: 0.7335 (t0) REVERT: C 210 LEU cc_start: 0.7668 (mm) cc_final: 0.7296 (pp) REVERT: C 755 ASP cc_start: 0.7533 (p0) cc_final: 0.6793 (m-30) REVERT: D 50 THR cc_start: 0.1519 (OUTLIER) cc_final: 0.1276 (m) REVERT: E 34 MET cc_start: 0.4754 (ppp) cc_final: 0.4387 (ppp) outliers start: 58 outliers final: 44 residues processed: 241 average time/residue: 0.3479 time to fit residues: 137.8501 Evaluate side-chains 235 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 187 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 227 optimal weight: 0.0050 chunk 263 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23237 Z= 0.200 Angle : 0.541 9.827 31707 Z= 0.282 Chirality : 0.044 0.193 3670 Planarity : 0.004 0.052 4133 Dihedral : 4.656 25.599 3201 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.60 % Allowed : 15.98 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 2967 helix: 1.44 (0.21), residues: 666 sheet: -0.56 (0.19), residues: 707 loop : -1.39 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 156 HIS 0.002 0.001 HIS C1193 PHE 0.019 0.001 PHE A 178 TYR 0.017 0.001 TYR C1159 ARG 0.009 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 199 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.5968 (mmtt) cc_final: 0.5465 (mptt) REVERT: A 687 VAL cc_start: 0.9300 (t) cc_final: 0.9076 (p) REVERT: A 956 LEU cc_start: 0.8794 (tp) cc_final: 0.8412 (tt) REVERT: A 1109 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: A 1121 MET cc_start: 0.8328 (tpp) cc_final: 0.7967 (tpp) REVERT: A 1217 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7488 (p0) REVERT: B 287 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7738 (ttpt) REVERT: B 306 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6611 (ttp-110) REVERT: B 1047 ASN cc_start: 0.7849 (m110) cc_final: 0.7388 (m-40) REVERT: B 1057 GLN cc_start: 0.8046 (mm110) cc_final: 0.7579 (mm-40) REVERT: B 1062 PHE cc_start: 0.8006 (m-80) cc_final: 0.7046 (m-80) REVERT: B 1231 ASP cc_start: 0.8020 (t0) cc_final: 0.7338 (t0) REVERT: C 210 LEU cc_start: 0.7640 (mm) cc_final: 0.7284 (pp) REVERT: C 361 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.5006 (t80) REVERT: D 50 THR cc_start: 0.1353 (OUTLIER) cc_final: 0.1084 (m) REVERT: E 34 MET cc_start: 0.4900 (ppp) cc_final: 0.4504 (ppp) outliers start: 62 outliers final: 49 residues processed: 244 average time/residue: 0.3129 time to fit residues: 125.2400 Evaluate side-chains 242 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1219 ASP Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 471 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.3980 chunk 252 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 211 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23237 Z= 0.219 Angle : 0.546 9.880 31707 Z= 0.285 Chirality : 0.044 0.196 3670 Planarity : 0.004 0.053 4133 Dihedral : 4.669 26.232 3201 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.47 % Allowed : 16.15 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 2967 helix: 1.42 (0.20), residues: 666 sheet: -0.56 (0.19), residues: 709 loop : -1.39 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 156 HIS 0.002 0.001 HIS C1193 PHE 0.019 0.001 PHE A 178 TYR 0.017 0.001 TYR C1159 ARG 0.006 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6035 (mmtt) cc_final: 0.5564 (mptt) REVERT: A 677 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 956 LEU cc_start: 0.8824 (tp) cc_final: 0.8438 (tt) REVERT: A 1109 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: A 1121 MET cc_start: 0.8304 (tpp) cc_final: 0.7929 (tpp) REVERT: A 1217 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7511 (p0) REVERT: B 306 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6594 (ttp-110) REVERT: B 1057 GLN cc_start: 0.7977 (mm110) cc_final: 0.7619 (mm-40) REVERT: B 1062 PHE cc_start: 0.8047 (m-80) cc_final: 0.7135 (m-80) REVERT: B 1231 ASP cc_start: 0.8022 (t0) cc_final: 0.7335 (t0) REVERT: C 210 LEU cc_start: 0.7656 (mm) cc_final: 0.7261 (pp) REVERT: C 361 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5053 (t80) REVERT: E 34 MET cc_start: 0.4957 (ppp) cc_final: 0.4568 (ppp) outliers start: 59 outliers final: 50 residues processed: 241 average time/residue: 0.3044 time to fit residues: 120.8560 Evaluate side-chains 245 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 879 GLN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 306 ARG Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1175 HIS C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23237 Z= 0.269 Angle : 0.577 13.209 31707 Z= 0.301 Chirality : 0.045 0.197 3670 Planarity : 0.004 0.053 4133 Dihedral : 4.774 27.522 3201 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.31 % Allowed : 16.40 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 2967 helix: 1.30 (0.20), residues: 667 sheet: -0.64 (0.19), residues: 701 loop : -1.41 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 156 HIS 0.003 0.001 HIS C1193 PHE 0.024 0.002 PHE C 286 TYR 0.017 0.001 TYR C1159 ARG 0.007 0.000 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 LYS cc_start: 0.6027 (mmtt) cc_final: 0.5574 (mptt) REVERT: A 677 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 956 LEU cc_start: 0.8835 (tp) cc_final: 0.8469 (tt) REVERT: A 1109 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: A 1121 MET cc_start: 0.8361 (tpp) cc_final: 0.8017 (tpp) REVERT: A 1183 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7428 (ttm110) REVERT: A 1217 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7550 (p0) REVERT: B 1057 GLN cc_start: 0.8005 (mm110) cc_final: 0.7607 (mm-40) REVERT: B 1062 PHE cc_start: 0.8034 (m-80) cc_final: 0.7354 (m-80) REVERT: B 1231 ASP cc_start: 0.8066 (t0) cc_final: 0.7245 (t0) REVERT: C 210 LEU cc_start: 0.7653 (mm) cc_final: 0.7239 (pp) REVERT: C 361 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.5039 (t80) REVERT: E 34 MET cc_start: 0.5007 (ppp) cc_final: 0.4613 (ppp) outliers start: 55 outliers final: 50 residues processed: 231 average time/residue: 0.3268 time to fit residues: 123.9603 Evaluate side-chains 239 residues out of total 2641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 185 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1109 GLU Chi-restraints excluded: chain A residue 1142 MET Chi-restraints excluded: chain A residue 1196 VAL Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1220 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain B residue 1234 GLN Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 698 ASN Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1173 ILE Chi-restraints excluded: chain C residue 1217 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 20.0000 chunk 253 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN ** C1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.130641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098298 restraints weight = 56983.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096985 restraints weight = 39734.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097426 restraints weight = 30815.442| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23237 Z= 0.265 Angle : 0.576 11.965 31707 Z= 0.301 Chirality : 0.045 0.188 3670 Planarity : 0.004 0.054 4133 Dihedral : 4.810 27.442 3201 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.43 % Allowed : 16.44 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 2967 helix: 1.28 (0.20), residues: 664 sheet: -0.67 (0.19), residues: 686 loop : -1.45 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 156 HIS 0.003 0.001 HIS C1193 PHE 0.024 0.002 PHE B 227 TYR 0.018 0.001 TYR C1159 ARG 0.006 0.000 ARG D 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3993.82 seconds wall clock time: 74 minutes 1.40 seconds (4441.40 seconds total)