Starting phenix.real_space_refine on Sat Mar 16 18:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4u_24178/03_2024/7n4u_24178_updated.pdb" } resolution = 3.34 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= 0.005 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 90 5.16 5 C 10068 2.51 5 N 2434 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 956": "OD1" <-> "OD2" Residue "A ASP 959": "OD1" <-> "OD2" Residue "A ASP 1018": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A ASP 1268": "OD1" <-> "OD2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 742": "NH1" <-> "NH2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B GLU 825": "OE1" <-> "OE2" Residue "B ASP 872": "OD1" <-> "OD2" Residue "B GLU 874": "OE1" <-> "OE2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 956": "OD1" <-> "OD2" Residue "B ASP 959": "OD1" <-> "OD2" Residue "B ASP 1018": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1199": "OE1" <-> "OE2" Residue "B ASP 1268": "OD1" <-> "OD2" Residue "B GLU 1276": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15396 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.34, per 1000 atoms: 0.54 Number of scatterers: 15396 At special positions: 0 Unit cell: (134.113, 89.131, 136.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2 15.00 O 2802 8.00 N 2434 7.00 C 10068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 966 " - pdb=" SG CYS B1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.03 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 Atom "HETATM15032 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM15265 O5 NAG B1602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A1075 " " NAG A1404 " - " ASN A 506 " " NAG B1602 " - " ASN B 431 " " NAG B1603 " - " ASN B 464 " " NAG B1604 " - " ASN B1075 " " NAG B1605 " - " ASN B 506 " " NAG C 1 " - " ASN A 497 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1037 " " NAG F 1 " - " ASN B 497 " " NAG G 1 " - " ASN B 909 " " NAG H 1 " - " ASN B1037 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 10 sheets defined 56.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.615A pdb=" N SER A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 372 Proline residue: A 362 - end of helix removed outlier: 4.734A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.728A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 584 through 606 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 628 through 631 No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.919A pdb=" N THR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 696 through 709 Proline residue: A 703 - end of helix removed outlier: 3.612A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 Processing helix chain 'A' and resid 732 through 763 Proline residue: A 745 - end of helix removed outlier: 4.510A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 803 removed outlier: 3.751A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 removed outlier: 5.418A pdb=" N ALA A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 843 through 865 removed outlier: 4.419A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.119A pdb=" N ILE A 919 " --> pdb=" O GLY A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.783A pdb=" N GLU A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1005 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1031 No H-bonds generated for 'chain 'A' and resid 1028 through 1031' Processing helix chain 'A' and resid 1059 through 1080 removed outlier: 3.552A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1108 through 1130 Proline residue: A1122 - end of helix removed outlier: 3.720A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1159 Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.450A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1225 removed outlier: 3.967A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1240 through 1265 removed outlier: 5.318A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'B' and resid 334 through 350 removed outlier: 3.619A pdb=" N SER B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 372 Proline residue: B 362 - end of helix removed outlier: 4.734A pdb=" N GLY B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 438 through 452 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 498 through 501 No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 518 through 527 removed outlier: 3.726A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 555 No H-bonds generated for 'chain 'B' and resid 552 through 555' Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 584 through 606 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 628 through 631 No H-bonds generated for 'chain 'B' and resid 628 through 631' Processing helix chain 'B' and resid 633 through 651 removed outlier: 3.919A pdb=" N THR B 638 " --> pdb=" O PRO B 634 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 663 No H-bonds generated for 'chain 'B' and resid 660 through 663' Processing helix chain 'B' and resid 666 through 689 Processing helix chain 'B' and resid 696 through 709 Proline residue: B 703 - end of helix removed outlier: 3.611A pdb=" N LEU B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 732 through 763 Proline residue: B 745 - end of helix removed outlier: 4.513A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 803 removed outlier: 3.749A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 792 " --> pdb=" O MET B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 840 removed outlier: 5.421A pdb=" N ALA B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Proline residue: B 838 - end of helix Processing helix chain 'B' and resid 843 through 865 removed outlier: 4.420A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.120A pdb=" N ILE B 919 " --> pdb=" O GLY B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.785A pdb=" N GLU B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 960 Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1005 through 1016 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1028 through 1031 No H-bonds generated for 'chain 'B' and resid 1028 through 1031' Processing helix chain 'B' and resid 1059 through 1080 removed outlier: 3.553A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1106 No H-bonds generated for 'chain 'B' and resid 1104 through 1106' Processing helix chain 'B' and resid 1108 through 1130 Proline residue: B1122 - end of helix removed outlier: 3.718A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1159 Processing helix chain 'B' and resid 1165 through 1190 removed outlier: 4.448A pdb=" N VAL B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B1181 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1225 removed outlier: 3.968A pdb=" N SER B1210 " --> pdb=" O ILE B1206 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B1211 " --> pdb=" O SER B1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix Processing helix chain 'B' and resid 1227 through 1229 No H-bonds generated for 'chain 'B' and resid 1227 through 1229' Processing helix chain 'B' and resid 1233 through 1238 Processing helix chain 'B' and resid 1240 through 1265 removed outlier: 5.323A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1271 through 1273 No H-bonds generated for 'chain 'B' and resid 1271 through 1273' Processing sheet with id= A, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= B, first strand: chain 'A' and resid 419 through 423 Processing sheet with id= C, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= D, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= E, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 409 through 411 Processing sheet with id= G, first strand: chain 'B' and resid 419 through 423 Processing sheet with id= H, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= I, first strand: chain 'B' and resid 1050 through 1052 Processing sheet with id= J, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 2046 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: 4.30 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2384 1.31 - 1.44: 4270 1.44 - 1.57: 8980 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15776 Sorted by residual: bond pdb=" C4 VIV B1608 " pdb=" O1 VIV B1608 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 VIV A1407 " pdb=" O1 VIV A1407 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.09e+01 bond pdb=" N VAL B 662 " pdb=" CA VAL B 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.07e+01 bond pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.69e+01 ... (remaining 15771 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.98: 547 106.98 - 113.86: 8741 113.86 - 120.75: 6900 120.75 - 127.63: 5222 127.63 - 134.51: 90 Bond angle restraints: 21500 Sorted by residual: angle pdb=" C GLY B 671 " pdb=" N GLY B 672 " pdb=" CA GLY B 672 " ideal model delta sigma weight residual 119.94 125.32 -5.38 1.11e+00 8.12e-01 2.35e+01 angle pdb=" C GLY A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 119.94 125.30 -5.36 1.11e+00 8.12e-01 2.33e+01 angle pdb=" C GLN A 342 " pdb=" N GLY A 343 " pdb=" CA GLY A 343 " ideal model delta sigma weight residual 119.94 125.09 -5.15 1.11e+00 8.12e-01 2.16e+01 angle pdb=" C GLN B 342 " pdb=" N GLY B 343 " pdb=" CA GLY B 343 " ideal model delta sigma weight residual 119.94 125.08 -5.14 1.11e+00 8.12e-01 2.15e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.04 -5.10 1.11e+00 8.12e-01 2.11e+01 ... (remaining 21495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 9440 31.97 - 63.95: 334 63.95 - 95.92: 54 95.92 - 127.89: 22 127.89 - 159.87: 2 Dihedral angle restraints: 9852 sinusoidal: 4300 harmonic: 5552 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.76 -66.76 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS B 966 " pdb=" SG CYS B 966 " pdb=" SG CYS B1024 " pdb=" CB CYS B1024 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 2526 0.948 - 1.896: 2 1.896 - 2.844: 2 2.844 - 3.792: 2 3.792 - 4.740: 8 Chirality restraints: 2540 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 ... (remaining 2537 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG G 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " 0.218 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C7 NAG B1602 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " -0.304 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " 0.169 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 190 2.66 - 3.22: 13908 3.22 - 3.78: 23980 3.78 - 4.34: 30549 4.34 - 4.90: 53896 Nonbonded interactions: 122523 Sorted by model distance: nonbonded pdb=" O VAL B 660 " pdb=" OD2 ASP B 808 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 660 " pdb=" OD2 ASP A 808 " model vdw 2.103 3.040 nonbonded pdb=" O VAL B 380 " pdb=" OG SER B 384 " model vdw 2.273 2.440 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.274 2.440 nonbonded pdb=" O MET A 661 " pdb=" N ASP A 808 " model vdw 2.360 2.520 ... (remaining 122518 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 333 through 1285 or resid 1402 through 1404 or resid 1406) \ ) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606) \ ) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.160 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.770 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.105 15776 Z= 0.920 Angle : 1.795 11.810 21500 Z= 1.328 Chirality : 0.294 4.740 2540 Planarity : 0.011 0.303 2650 Dihedral : 17.763 159.868 6236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 1.79 % Allowed : 7.52 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.17), residues: 1902 helix: -1.48 (0.13), residues: 1062 sheet: -2.56 (0.40), residues: 126 loop : -1.97 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 518 HIS 0.005 0.002 HIS B 521 PHE 0.040 0.002 PHE A 791 TYR 0.033 0.003 TYR B1062 ARG 0.006 0.001 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.8461 (t0) cc_final: 0.7944 (t0) REVERT: A 524 TYR cc_start: 0.7666 (t80) cc_final: 0.7206 (t80) REVERT: A 566 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7456 (mp0) REVERT: A 818 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 994 MET cc_start: 0.7523 (ptp) cc_final: 0.7119 (ppp) REVERT: A 998 MET cc_start: 0.7203 (pmm) cc_final: 0.6584 (pmm) REVERT: A 1102 TYR cc_start: 0.8478 (m-10) cc_final: 0.8015 (m-10) REVERT: A 1103 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: A 1198 LEU cc_start: 0.7637 (mt) cc_final: 0.7296 (tt) REVERT: A 1242 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6458 (tt) REVERT: B 476 ASN cc_start: 0.8353 (t0) cc_final: 0.7817 (t0) REVERT: B 524 TYR cc_start: 0.7651 (t80) cc_final: 0.7172 (t80) REVERT: B 566 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 818 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 994 MET cc_start: 0.7248 (ptp) cc_final: 0.6880 (ppp) REVERT: B 998 MET cc_start: 0.7291 (pmm) cc_final: 0.6676 (pmm) REVERT: B 1102 TYR cc_start: 0.8474 (m-10) cc_final: 0.7981 (m-10) REVERT: B 1198 LEU cc_start: 0.7681 (mt) cc_final: 0.7426 (tt) outliers start: 29 outliers final: 11 residues processed: 206 average time/residue: 0.2570 time to fit residues: 81.0282 Evaluate side-chains 135 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 872 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 409 GLN A 527 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS A1233 GLN A1253 HIS B 339 GLN B 409 GLN B 476 ASN B 527 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1184 HIS B1220 ASN B1233 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15776 Z= 0.176 Angle : 0.691 13.326 21500 Z= 0.309 Chirality : 0.054 1.032 2540 Planarity : 0.004 0.042 2650 Dihedral : 13.394 132.564 2887 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 3.02 % Allowed : 11.65 % Favored : 85.33 % 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: -0.33 (0.19), residues: 1902 helix: 0.73 (0.16), residues: 1058 sheet: -1.96 (0.43), residues: 126 loop : -1.25 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.004 0.001 HIS B1053 PHE 0.018 0.001 PHE B 930 TYR 0.012 0.001 TYR B 646 ARG 0.007 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.643 Fit side-chains REVERT: A 476 ASN cc_start: 0.8426 (t0) cc_final: 0.7935 (t0) REVERT: A 524 TYR cc_start: 0.7416 (t80) cc_final: 0.6982 (t80) REVERT: A 566 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7420 (mp0) REVERT: A 607 MET cc_start: 0.8262 (mmm) cc_final: 0.7370 (mmm) REVERT: A 818 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 994 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7166 (ppp) REVERT: A 998 MET cc_start: 0.7165 (pmm) cc_final: 0.6367 (pmm) REVERT: A 1023 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8273 (mttp) REVERT: A 1102 TYR cc_start: 0.8350 (m-10) cc_final: 0.7791 (m-10) REVERT: A 1198 LEU cc_start: 0.7987 (mt) cc_final: 0.7662 (tt) REVERT: B 476 ASN cc_start: 0.8297 (t0) cc_final: 0.7803 (t0) REVERT: B 524 TYR cc_start: 0.7538 (t80) cc_final: 0.7076 (t80) REVERT: B 566 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7428 (mp0) REVERT: B 607 MET cc_start: 0.7972 (mmm) cc_final: 0.7020 (mmm) REVERT: B 994 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6821 (ppp) REVERT: B 1023 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8369 (mttp) REVERT: B 1102 TYR cc_start: 0.8341 (m-10) cc_final: 0.7770 (m-10) REVERT: B 1103 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: B 1198 LEU cc_start: 0.7921 (mt) cc_final: 0.7706 (tt) outliers start: 49 outliers final: 21 residues processed: 182 average time/residue: 0.2229 time to fit residues: 65.4991 Evaluate side-chains 142 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 ASN B1253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15776 Z= 0.264 Angle : 0.637 10.590 21500 Z= 0.293 Chirality : 0.048 0.820 2540 Planarity : 0.003 0.029 2650 Dihedral : 11.021 115.998 2875 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.33 % Allowed : 12.76 % Favored : 83.91 % 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: 0.09 (0.20), residues: 1902 helix: 1.08 (0.16), residues: 1048 sheet: -1.98 (0.47), residues: 102 loop : -1.06 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS B1053 PHE 0.018 0.001 PHE A 930 TYR 0.013 0.001 TYR B 646 ARG 0.003 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 122 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.8430 (t0) cc_final: 0.7969 (t0) REVERT: A 524 TYR cc_start: 0.7461 (t80) cc_final: 0.6982 (t80) REVERT: A 566 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7495 (mp0) REVERT: A 818 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 994 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7096 (ppp) REVERT: A 998 MET cc_start: 0.7203 (pmm) cc_final: 0.6538 (pmm) REVERT: A 1102 TYR cc_start: 0.8495 (m-10) cc_final: 0.8038 (m-10) REVERT: A 1128 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7964 (m) REVERT: A 1198 LEU cc_start: 0.8002 (mt) cc_final: 0.7662 (tt) REVERT: B 476 ASN cc_start: 0.8386 (t0) cc_final: 0.7859 (t0) REVERT: B 524 TYR cc_start: 0.7549 (t80) cc_final: 0.7045 (t80) REVERT: B 566 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7413 (mp0) REVERT: B 994 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6959 (ppp) REVERT: B 1102 TYR cc_start: 0.8499 (m-10) cc_final: 0.8040 (m-10) REVERT: B 1128 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 1198 LEU cc_start: 0.7939 (mt) cc_final: 0.7712 (tt) outliers start: 54 outliers final: 36 residues processed: 158 average time/residue: 0.2406 time to fit residues: 60.1215 Evaluate side-chains 154 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1224 ILE Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 49 optimal weight: 0.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15776 Z= 0.174 Angle : 0.558 10.641 21500 Z= 0.260 Chirality : 0.043 0.675 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.995 107.505 2872 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.90 % Rotamer: Outliers : 3.08 % Allowed : 13.81 % Favored : 83.11 % 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: 0.34 (0.20), residues: 1902 helix: 1.20 (0.16), residues: 1060 sheet: -1.78 (0.49), residues: 102 loop : -0.86 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 PHE 0.013 0.001 PHE A 930 TYR 0.012 0.001 TYR B 646 ARG 0.004 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 120 time to evaluate : 1.603 Fit side-chains REVERT: A 476 ASN cc_start: 0.8528 (t0) cc_final: 0.8073 (t0) REVERT: A 524 TYR cc_start: 0.7455 (t80) cc_final: 0.6997 (t80) REVERT: A 566 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7380 (mp0) REVERT: A 607 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7118 (mmm) REVERT: A 818 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8369 (tp) REVERT: A 994 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7107 (ppp) REVERT: A 998 MET cc_start: 0.7207 (pmm) cc_final: 0.6556 (pmm) REVERT: A 1102 TYR cc_start: 0.8486 (m-10) cc_final: 0.8102 (m-10) REVERT: A 1128 CYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 1198 LEU cc_start: 0.8031 (mt) cc_final: 0.7696 (tt) REVERT: B 476 ASN cc_start: 0.8378 (t0) cc_final: 0.7877 (t0) REVERT: B 524 TYR cc_start: 0.7561 (t80) cc_final: 0.7079 (t80) REVERT: B 566 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7343 (mp0) REVERT: B 607 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7053 (mmm) REVERT: B 994 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6974 (ppp) REVERT: B 1102 TYR cc_start: 0.8440 (m-10) cc_final: 0.7983 (m-10) REVERT: B 1128 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8004 (m) REVERT: B 1198 LEU cc_start: 0.7960 (mt) cc_final: 0.7718 (tt) outliers start: 50 outliers final: 28 residues processed: 155 average time/residue: 0.2353 time to fit residues: 58.2098 Evaluate side-chains 145 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15776 Z= 0.347 Angle : 0.629 10.283 21500 Z= 0.297 Chirality : 0.045 0.604 2540 Planarity : 0.003 0.031 2650 Dihedral : 9.956 102.964 2872 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.79 % Rotamer: Outliers : 3.95 % Allowed : 14.49 % Favored : 81.57 % 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: -0.06 (0.20), residues: 1902 helix: 0.92 (0.16), residues: 1058 sheet: -2.11 (0.47), residues: 106 loop : -1.07 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 592 HIS 0.004 0.001 HIS B1053 PHE 0.017 0.002 PHE B 791 TYR 0.015 0.001 TYR A 420 ARG 0.003 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 112 time to evaluate : 1.732 Fit side-chains REVERT: A 476 ASN cc_start: 0.8504 (t0) cc_final: 0.8034 (t0) REVERT: A 524 TYR cc_start: 0.7561 (t80) cc_final: 0.7040 (t80) REVERT: A 566 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7434 (mp0) REVERT: A 607 MET cc_start: 0.7672 (mmm) cc_final: 0.7101 (mmm) REVERT: A 818 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 836 TYR cc_start: 0.7629 (t80) cc_final: 0.7229 (t80) REVERT: A 994 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7182 (ppp) REVERT: A 998 MET cc_start: 0.7260 (pmm) cc_final: 0.6584 (pmm) REVERT: A 1023 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8364 (mttp) REVERT: A 1102 TYR cc_start: 0.8626 (m-10) cc_final: 0.8336 (m-10) REVERT: A 1128 CYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7980 (m) REVERT: A 1130 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 1198 LEU cc_start: 0.7961 (mt) cc_final: 0.7649 (tt) REVERT: B 476 ASN cc_start: 0.8448 (t0) cc_final: 0.7946 (t0) REVERT: B 524 TYR cc_start: 0.7546 (t80) cc_final: 0.6994 (t80) REVERT: B 566 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7372 (mp0) REVERT: B 994 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6963 (ppp) REVERT: B 1023 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8450 (mttp) REVERT: B 1102 TYR cc_start: 0.8554 (m-10) cc_final: 0.8197 (m-10) REVERT: B 1128 CYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7950 (m) REVERT: B 1198 LEU cc_start: 0.7967 (mt) cc_final: 0.7754 (tt) outliers start: 64 outliers final: 40 residues processed: 159 average time/residue: 0.2503 time to fit residues: 63.3653 Evaluate side-chains 157 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1224 ILE Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15776 Z= 0.160 Angle : 0.536 10.357 21500 Z= 0.251 Chirality : 0.042 0.568 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.501 105.637 2872 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.21 % Allowed : 15.91 % Favored : 80.89 % 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: 0.23 (0.20), residues: 1902 helix: 1.16 (0.16), residues: 1054 sheet: -1.99 (0.48), residues: 106 loop : -0.93 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 518 HIS 0.002 0.001 HIS A1053 PHE 0.015 0.001 PHE A 839 TYR 0.010 0.001 TYR B 646 ARG 0.003 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 1.835 Fit side-chains REVERT: A 476 ASN cc_start: 0.8468 (t0) cc_final: 0.8020 (t0) REVERT: A 524 TYR cc_start: 0.7527 (t80) cc_final: 0.6983 (t80) REVERT: A 566 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7432 (mp0) REVERT: A 607 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7060 (mmm) REVERT: A 818 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8362 (tp) REVERT: A 836 TYR cc_start: 0.7580 (t80) cc_final: 0.7171 (t80) REVERT: A 994 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7118 (ppp) REVERT: A 998 MET cc_start: 0.7265 (pmm) cc_final: 0.6623 (pmm) REVERT: A 1023 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8391 (mttp) REVERT: A 1102 TYR cc_start: 0.8557 (m-10) cc_final: 0.8189 (m-10) REVERT: A 1128 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7990 (m) REVERT: A 1198 LEU cc_start: 0.8005 (mt) cc_final: 0.7676 (tt) REVERT: B 476 ASN cc_start: 0.8388 (t0) cc_final: 0.7914 (t0) REVERT: B 524 TYR cc_start: 0.7565 (t80) cc_final: 0.6996 (t80) REVERT: B 566 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7349 (mp0) REVERT: B 994 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6945 (ppp) REVERT: B 1023 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8473 (mttp) REVERT: B 1102 TYR cc_start: 0.8446 (m-10) cc_final: 0.8013 (m-10) REVERT: B 1128 CYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7987 (m) REVERT: B 1198 LEU cc_start: 0.7971 (mt) cc_final: 0.7744 (tt) outliers start: 52 outliers final: 33 residues processed: 145 average time/residue: 0.2399 time to fit residues: 55.1337 Evaluate side-chains 144 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 0.0670 chunk 134 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15776 Z= 0.153 Angle : 0.514 10.217 21500 Z= 0.242 Chirality : 0.041 0.519 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.188 105.049 2872 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.02 % Allowed : 16.03 % Favored : 80.95 % 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: 0.47 (0.20), residues: 1902 helix: 1.32 (0.16), residues: 1054 sheet: -1.82 (0.49), residues: 106 loop : -0.77 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 518 HIS 0.002 0.001 HIS A1053 PHE 0.021 0.001 PHE A 839 TYR 0.015 0.001 TYR A1105 ARG 0.003 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 109 time to evaluate : 1.456 Fit side-chains REVERT: A 476 ASN cc_start: 0.8406 (t0) cc_final: 0.7972 (t0) REVERT: A 524 TYR cc_start: 0.7534 (t80) cc_final: 0.6969 (t80) REVERT: A 566 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7365 (mp0) REVERT: A 607 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7070 (mmm) REVERT: A 994 MET cc_start: 0.7594 (ptp) cc_final: 0.7035 (ppp) REVERT: A 998 MET cc_start: 0.7248 (pmm) cc_final: 0.6594 (pmm) REVERT: A 1023 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: A 1102 TYR cc_start: 0.8557 (m-10) cc_final: 0.8269 (m-10) REVERT: A 1128 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8011 (m) REVERT: A 1198 LEU cc_start: 0.8049 (mt) cc_final: 0.7737 (tt) REVERT: A 1282 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: B 476 ASN cc_start: 0.8329 (t0) cc_final: 0.7871 (t0) REVERT: B 524 TYR cc_start: 0.7574 (t80) cc_final: 0.6971 (t80) REVERT: B 566 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7354 (mp0) REVERT: B 994 MET cc_start: 0.7395 (ptp) cc_final: 0.7019 (ppp) REVERT: B 1023 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8347 (mttp) REVERT: B 1102 TYR cc_start: 0.8446 (m-10) cc_final: 0.7973 (m-10) REVERT: B 1128 CYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 1198 LEU cc_start: 0.8015 (mt) cc_final: 0.7778 (tt) REVERT: B 1282 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6749 (pm20) outliers start: 49 outliers final: 33 residues processed: 145 average time/residue: 0.2324 time to fit residues: 53.0384 Evaluate side-chains 145 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 0.0040 chunk 175 optimal weight: 8.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15776 Z= 0.195 Angle : 0.525 10.239 21500 Z= 0.248 Chirality : 0.041 0.497 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.120 104.364 2870 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.21 % Allowed : 16.03 % Favored : 80.76 % 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: 0.47 (0.20), residues: 1902 helix: 1.31 (0.16), residues: 1054 sheet: -1.83 (0.48), residues: 106 loop : -0.76 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 592 HIS 0.002 0.000 HIS A1053 PHE 0.017 0.001 PHE A 839 TYR 0.011 0.001 TYR B 646 ARG 0.002 0.000 ARG A1067 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 1.639 Fit side-chains REVERT: A 476 ASN cc_start: 0.8404 (t0) cc_final: 0.7968 (t0) REVERT: A 524 TYR cc_start: 0.7552 (t80) cc_final: 0.6963 (t80) REVERT: A 566 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7362 (mp0) REVERT: A 607 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6972 (mmm) REVERT: A 994 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7050 (ppp) REVERT: A 998 MET cc_start: 0.7274 (pmm) cc_final: 0.6736 (pmm) REVERT: A 1023 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: A 1102 TYR cc_start: 0.8584 (m-10) cc_final: 0.8315 (m-10) REVERT: A 1128 CYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7997 (m) REVERT: A 1198 LEU cc_start: 0.8033 (mt) cc_final: 0.7720 (tt) REVERT: A 1282 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: B 476 ASN cc_start: 0.8317 (t0) cc_final: 0.7864 (t0) REVERT: B 524 TYR cc_start: 0.7563 (t80) cc_final: 0.6963 (t80) REVERT: B 566 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7364 (mp0) REVERT: B 994 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6915 (ppp) REVERT: B 1023 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8402 (mttp) REVERT: B 1102 TYR cc_start: 0.8493 (m-10) cc_final: 0.8044 (m-10) REVERT: B 1128 CYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7984 (m) REVERT: B 1198 LEU cc_start: 0.8028 (mt) cc_final: 0.7797 (tt) REVERT: B 1282 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6762 (pm20) outliers start: 52 outliers final: 38 residues processed: 142 average time/residue: 0.2556 time to fit residues: 56.1489 Evaluate side-chains 151 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 104 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 10.0000 chunk 170 optimal weight: 0.0970 chunk 175 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15776 Z= 0.192 Angle : 0.527 10.239 21500 Z= 0.248 Chirality : 0.041 0.486 2540 Planarity : 0.003 0.027 2650 Dihedral : 8.962 104.390 2870 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.21 % Allowed : 16.21 % Favored : 80.58 % 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: 0.53 (0.20), residues: 1902 helix: 1.35 (0.16), residues: 1054 sheet: -1.86 (0.48), residues: 106 loop : -0.72 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 PHE 0.018 0.001 PHE A 839 TYR 0.011 0.001 TYR B 493 ARG 0.002 0.000 ARG A 742 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 1.522 Fit side-chains REVERT: A 476 ASN cc_start: 0.8400 (t0) cc_final: 0.7972 (t0) REVERT: A 524 TYR cc_start: 0.7553 (t80) cc_final: 0.6950 (t80) REVERT: A 566 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7361 (mp0) REVERT: A 607 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6900 (mmm) REVERT: A 994 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: A 998 MET cc_start: 0.7268 (pmm) cc_final: 0.6738 (pmm) REVERT: A 1023 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8358 (mttp) REVERT: A 1102 TYR cc_start: 0.8589 (m-10) cc_final: 0.8306 (m-10) REVERT: A 1128 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7976 (m) REVERT: A 1198 LEU cc_start: 0.8034 (mt) cc_final: 0.7724 (tt) REVERT: A 1282 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: B 476 ASN cc_start: 0.8321 (t0) cc_final: 0.7872 (t0) REVERT: B 524 TYR cc_start: 0.7565 (t80) cc_final: 0.6961 (t80) REVERT: B 566 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7348 (mp0) REVERT: B 994 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7093 (ppp) REVERT: B 1023 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8404 (mttp) REVERT: B 1102 TYR cc_start: 0.8487 (m-10) cc_final: 0.8041 (m-10) REVERT: B 1128 CYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7985 (m) REVERT: B 1198 LEU cc_start: 0.8000 (mt) cc_final: 0.7767 (tt) REVERT: B 1282 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6768 (pm20) outliers start: 52 outliers final: 39 residues processed: 142 average time/residue: 0.2360 time to fit residues: 52.9823 Evaluate side-chains 153 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 105 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 174 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15776 Z= 0.222 Angle : 0.547 10.238 21500 Z= 0.256 Chirality : 0.041 0.469 2540 Planarity : 0.003 0.028 2650 Dihedral : 8.917 103.756 2870 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.08 % Allowed : 16.52 % Favored : 80.39 % 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: 0.52 (0.20), residues: 1902 helix: 1.39 (0.16), residues: 1044 sheet: -1.89 (0.48), residues: 106 loop : -0.75 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 592 HIS 0.003 0.001 HIS A1053 PHE 0.022 0.001 PHE B 839 TYR 0.011 0.001 TYR B 646 ARG 0.002 0.000 ARG B1200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 104 time to evaluate : 1.755 Fit side-chains REVERT: A 476 ASN cc_start: 0.8383 (t0) cc_final: 0.7939 (t0) REVERT: A 524 TYR cc_start: 0.7575 (t80) cc_final: 0.6975 (t80) REVERT: A 566 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7374 (mp0) REVERT: A 607 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6885 (mmm) REVERT: A 994 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7111 (ppp) REVERT: A 998 MET cc_start: 0.7294 (pmm) cc_final: 0.6782 (pmm) REVERT: A 1023 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8321 (mttp) REVERT: A 1102 TYR cc_start: 0.8595 (m-10) cc_final: 0.8251 (m-10) REVERT: A 1128 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 1198 LEU cc_start: 0.8002 (mt) cc_final: 0.7717 (tt) REVERT: A 1282 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: B 476 ASN cc_start: 0.8358 (t0) cc_final: 0.7909 (t0) REVERT: B 524 TYR cc_start: 0.7569 (t80) cc_final: 0.6961 (t80) REVERT: B 566 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7331 (mp0) REVERT: B 994 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7151 (ppp) REVERT: B 1023 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8441 (mttp) REVERT: B 1102 TYR cc_start: 0.8540 (m-10) cc_final: 0.8094 (m-10) REVERT: B 1128 CYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 1198 LEU cc_start: 0.8008 (mt) cc_final: 0.7777 (tt) REVERT: B 1282 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6832 (pm20) outliers start: 50 outliers final: 39 residues processed: 139 average time/residue: 0.2447 time to fit residues: 53.2264 Evaluate side-chains 151 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 103 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 994 MET Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1107 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 0.0000 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.113893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085098 restraints weight = 25987.299| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.82 r_work: 0.3104 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15776 Z= 0.173 Angle : 0.517 10.275 21500 Z= 0.243 Chirality : 0.040 0.457 2540 Planarity : 0.003 0.027 2650 Dihedral : 8.719 104.483 2870 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.96 % Allowed : 16.89 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1902 helix: 1.47 (0.16), residues: 1044 sheet: -1.87 (0.48), residues: 106 loop : -0.67 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 PHE 0.019 0.001 PHE B 839 TYR 0.010 0.001 TYR A1105 ARG 0.002 0.000 ARG A1067 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.99 seconds wall clock time: 53 minutes 49.03 seconds (3229.03 seconds total)