Starting phenix.real_space_refine on Fri Feb 16 13:11:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4v_24179/02_2024/7n4v_24179_updated.pdb" } resolution = 3.58 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= 0.045 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 10064 2.51 5 N 2434 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A ASP 880": "OD1" <-> "OD2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1006": "OE1" <-> "OE2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ASP 1087": "OD1" <-> "OD2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 712": "OD1" <-> "OD2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 742": "NH1" <-> "NH2" Residue "B ASP 872": "OD1" <-> "OD2" Residue "B ASP 880": "OD1" <-> "OD2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1006": "OE1" <-> "OE2" Residue "B TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1064": "OE1" <-> "OE2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ASP 1087": "OD1" <-> "OD2" Residue "B PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1136": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15390 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 8.95, per 1000 atoms: 0.58 Number of scatterers: 15390 At special positions: 0 Unit cell: (109.956, 133.28, 134.946, 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 2800 8.00 N 2434 7.00 C 10064 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=2.04 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=2.04 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=2.91 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 6.75 Conformation dependent library (CDL) restraints added in 2.8 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: 79 helices and 8 sheets defined 56.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 352 through 372 Proline residue: A 362 - end of helix removed outlier: 4.778A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.349A 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 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 490 through 494 removed outlier: 3.745A pdb=" N TYR A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) 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: 3.516A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' 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 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.790A 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 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 702 through 710 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: 4.657A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 803 removed outlier: 3.715A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 removed outlier: 5.337A 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: 4.693A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.868A 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 1005 through 1017 Proline residue: A1013 - end of helix removed outlier: 3.577A pdb=" N ASN A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1032 No H-bonds generated for 'chain 'A' and resid 1029 through 1032' Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.538A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' 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: 3.593A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1159 removed outlier: 4.146A pdb=" N LEU A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.236A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1229 removed outlier: 4.147A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 4.330A pdb=" N VAL A1226 " --> pdb=" O PRO A1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1240 through 1265 removed outlier: 4.704A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1278 through 1280 No H-bonds generated for 'chain 'A' and resid 1278 through 1280' Processing helix chain 'B' and resid 334 through 350 Processing helix chain 'B' and resid 352 through 372 Proline residue: B 362 - end of helix removed outlier: 4.778A pdb=" N GLY B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.350A 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 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.744A pdb=" N TYR B 493 " --> pdb=" O LEU B 490 " (cutoff:3.500A) 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: 3.517A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' 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 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 633 through 651 removed outlier: 3.789A 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 710 removed outlier: 4.219A pdb=" N VAL B 701 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Proline residue: B 703 - end of helix 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: 4.659A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 803 removed outlier: 3.716A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL B 792 " --> pdb=" O MET B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 840 removed outlier: 5.337A 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: 4.692A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 930 through 939 removed outlier: 3.868A 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 1005 through 1017 Proline residue: B1013 - end of helix removed outlier: 3.575A pdb=" N ASN B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1032 No H-bonds generated for 'chain 'B' and resid 1029 through 1032' Processing helix chain 'B' and resid 1059 through 1082 removed outlier: 3.535A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1099 No H-bonds generated for 'chain 'B' and resid 1097 through 1099' 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: 3.593A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1159 removed outlier: 4.150A pdb=" N LEU B1140 " --> pdb=" O ARG B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1190 removed outlier: 4.236A pdb=" N VAL B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B1181 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1229 removed outlier: 4.145A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix removed outlier: 4.330A pdb=" N VAL B1226 " --> pdb=" O PRO B1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B1227 " --> pdb=" O GLY B1223 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B1228 " --> pdb=" O ILE B1224 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B1229 " --> pdb=" O LEU B1225 " (cutoff:3.500A) Processing helix chain 'B' and resid 1233 through 1238 Processing helix chain 'B' and resid 1240 through 1265 removed outlier: 4.708A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1278 through 1280 No H-bonds generated for 'chain 'B' and resid 1278 through 1280' Processing sheet with id= A, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.570A pdb=" N LYS A 430 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= C, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= D, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.569A pdb=" N LYS B 430 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 505 through 509 Processing sheet with id= G, first strand: chain 'B' and resid 1050 through 1052 Processing sheet with id= H, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 690 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: 5.07 Time building geometry restraints manager: 7.24 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: 2382 1.31 - 1.44: 4275 1.44 - 1.57: 8975 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15774 Sorted by residual: bond pdb=" N ILE B 470 " pdb=" CA ILE B 470 " ideal model delta sigma weight residual 1.456 1.500 -0.044 9.50e-03 1.11e+04 2.13e+01 bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.043 9.50e-03 1.11e+04 2.05e+01 bond pdb=" N VAL A 701 " pdb=" CA VAL A 701 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.97e+01 bond pdb=" N VAL B 701 " pdb=" CA VAL B 701 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N LEU A1012 " pdb=" CA LEU A1012 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.80e+01 ... (remaining 15769 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.23: 507 106.23 - 113.30: 8441 113.30 - 120.36: 6944 120.36 - 127.42: 5522 127.42 - 134.48: 92 Bond angle restraints: 21506 Sorted by residual: angle pdb=" C ALA B 914 " pdb=" N GLY B 915 " pdb=" CA GLY B 915 " ideal model delta sigma weight residual 119.94 125.22 -5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" C SER B 433 " pdb=" N GLY B 434 " pdb=" CA GLY B 434 " ideal model delta sigma weight residual 119.98 125.24 -5.26 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.19 -5.25 1.11e+00 8.12e-01 2.24e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 angle pdb=" C SER B1137 " pdb=" N GLY B1138 " pdb=" CA GLY B1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 9490 30.32 - 60.63: 363 60.63 - 90.95: 55 90.95 - 121.27: 16 121.27 - 151.59: 2 Dihedral angle restraints: 9926 sinusoidal: 4374 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 93.00 162.69 -69.69 1 1.00e+01 1.00e-02 6.27e+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 93.00 162.66 -69.66 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS A 966 " pdb=" SG CYS A 966 " pdb=" SG CYS A1024 " pdb=" CB CYS A1024 " ideal model delta sinusoidal sigma weight residual 93.00 158.05 -65.05 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 9923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2546 0.932 - 1.864: 0 1.864 - 2.796: 0 2.796 - 3.727: 0 3.727 - 4.659: 4 Chirality restraints: 2550 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 2.26 -4.66 2.00e-02 2.50e+03 5.43e+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 2.26 -4.66 2.00e-02 2.50e+03 5.42e+04 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 2.24 -4.64 2.00e-01 2.50e+01 5.37e+02 ... (remaining 2547 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " -0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1401 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG A1401 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1401 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A1401 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG A1401 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.252 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG F 1 " 0.135 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.202 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.319 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2181 2.81 - 3.33: 16380 3.33 - 3.86: 23933 3.86 - 4.38: 30470 4.38 - 4.90: 50183 Nonbonded interactions: 123147 Sorted by model distance: nonbonded pdb=" ND2 ASN A1170 " pdb=" O PHE A1238 " model vdw 2.288 2.520 nonbonded pdb=" ND2 ASN B1170 " pdb=" O PHE B1238 " model vdw 2.289 2.520 nonbonded pdb=" OG SER B 433 " pdb=" O ALA B 567 " model vdw 2.308 2.440 nonbonded pdb=" OG SER A 433 " pdb=" O ALA A 567 " model vdw 2.309 2.440 nonbonded pdb=" O SER B1207 " pdb=" OG SER B1210 " model vdw 2.313 2.440 ... (remaining 123142 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 \ through 1407)) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606 \ through 1607)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 10.250 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.130 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 0.073 15774 Z= 0.913 Angle : 1.776 11.833 21506 Z= 1.307 Chirality : 0.203 4.659 2550 Planarity : 0.012 0.290 2648 Dihedral : 16.543 151.585 6310 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % 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: -3.22 (0.16), residues: 1902 helix: -1.55 (0.13), residues: 1052 sheet: -3.15 (0.33), residues: 130 loop : -2.66 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 457 HIS 0.010 0.003 HIS B1184 PHE 0.027 0.003 PHE A 791 TYR 0.029 0.003 TYR A 646 ARG 0.004 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 198 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8582 (t80) cc_final: 0.8342 (t80) REVERT: A 487 ILE cc_start: 0.8406 (mt) cc_final: 0.8101 (mp) REVERT: A 623 ASP cc_start: 0.7479 (t0) cc_final: 0.7071 (t0) REVERT: A 743 VAL cc_start: 0.7736 (m) cc_final: 0.7504 (p) REVERT: A 894 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: A 1011 TYR cc_start: 0.7871 (m-10) cc_final: 0.7294 (m-10) REVERT: A 1218 MET cc_start: 0.8177 (mmt) cc_final: 0.7951 (mmm) REVERT: B 457 TRP cc_start: 0.6069 (t-100) cc_final: 0.5225 (t-100) REVERT: B 588 GLN cc_start: 0.8065 (mt0) cc_final: 0.7631 (mm-40) REVERT: B 591 LEU cc_start: 0.8114 (mt) cc_final: 0.7863 (mt) REVERT: B 894 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: B 1064 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6493 (mp0) REVERT: B 1091 GLU cc_start: 0.7366 (pt0) cc_final: 0.6999 (tt0) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2838 time to fit residues: 82.8341 Evaluate side-chains 135 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 894 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 488 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 GLN B 339 GLN B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1043 GLN B1236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15774 Z= 0.200 Angle : 0.689 14.708 21506 Z= 0.310 Chirality : 0.047 0.725 2550 Planarity : 0.004 0.039 2648 Dihedral : 12.290 130.454 2936 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.36 % Allowed : 10.30 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1902 helix: 0.33 (0.16), residues: 1076 sheet: -2.55 (0.37), residues: 132 loop : -1.81 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 347 HIS 0.005 0.001 HIS A1009 PHE 0.024 0.001 PHE B 930 TYR 0.018 0.001 TYR A 886 ARG 0.004 0.000 ARG B 693 *********************** 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 170 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 GLN cc_start: 0.8770 (mt0) cc_final: 0.8401 (mt0) REVERT: A 422 TYR cc_start: 0.8665 (t80) cc_final: 0.8254 (t80) REVERT: A 457 TRP cc_start: 0.6655 (t-100) cc_final: 0.5796 (t-100) REVERT: A 610 MET cc_start: 0.7968 (ttm) cc_final: 0.7619 (ttp) REVERT: A 783 ASP cc_start: 0.7578 (t70) cc_final: 0.7303 (t0) REVERT: A 1011 TYR cc_start: 0.8007 (m-10) cc_final: 0.7415 (m-80) REVERT: A 1050 MET cc_start: 0.8803 (ttt) cc_final: 0.8587 (ttt) REVERT: B 457 TRP cc_start: 0.6186 (t-100) cc_final: 0.5414 (t-100) REVERT: B 588 GLN cc_start: 0.8064 (mt0) cc_final: 0.7565 (mm-40) REVERT: B 591 LEU cc_start: 0.8058 (mt) cc_final: 0.7843 (mt) REVERT: B 610 MET cc_start: 0.8196 (ttm) cc_final: 0.7925 (ttp) REVERT: B 894 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: B 1091 GLU cc_start: 0.7092 (pt0) cc_final: 0.6858 (tt0) outliers start: 22 outliers final: 7 residues processed: 163 average time/residue: 0.2422 time to fit residues: 61.6483 Evaluate side-chains 142 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 172 optimal weight: 0.0980 chunk 186 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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** A1009 HIS ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 GLN B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15774 Z= 0.189 Angle : 0.594 9.641 21506 Z= 0.276 Chirality : 0.042 0.324 2550 Planarity : 0.004 0.042 2648 Dihedral : 9.941 118.836 2934 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.91 % Allowed : 11.84 % Favored : 86.25 % 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: -0.45 (0.20), residues: 1902 helix: 0.76 (0.16), residues: 1074 sheet: -2.25 (0.39), residues: 132 loop : -1.52 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1014 HIS 0.003 0.001 HIS A1184 PHE 0.019 0.001 PHE B 930 TYR 0.018 0.001 TYR A 646 ARG 0.004 0.000 ARG A 693 *********************** 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 175 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8665 (t80) cc_final: 0.8208 (t80) REVERT: A 457 TRP cc_start: 0.6544 (t-100) cc_final: 0.5698 (t-100) REVERT: A 610 MET cc_start: 0.7978 (ttm) cc_final: 0.7595 (ttp) REVERT: A 707 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6462 (tt) REVERT: A 783 ASP cc_start: 0.7596 (t70) cc_final: 0.7322 (t0) REVERT: A 1008 PHE cc_start: 0.8385 (t80) cc_final: 0.8140 (t80) REVERT: A 1011 TYR cc_start: 0.7762 (m-10) cc_final: 0.7441 (m-80) REVERT: A 1050 MET cc_start: 0.8829 (ttt) cc_final: 0.8563 (ttt) REVERT: A 1064 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6348 (mp0) REVERT: B 457 TRP cc_start: 0.6077 (t-100) cc_final: 0.5395 (t-100) REVERT: B 579 TYR cc_start: 0.7577 (m-80) cc_final: 0.7048 (m-80) REVERT: B 588 GLN cc_start: 0.8041 (mt0) cc_final: 0.7597 (mm-40) REVERT: B 610 MET cc_start: 0.8113 (ttm) cc_final: 0.7799 (ttp) REVERT: B 766 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7583 (mmt) REVERT: B 894 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: B 1064 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6235 (mp0) REVERT: B 1091 GLU cc_start: 0.7021 (pt0) cc_final: 0.6813 (tt0) outliers start: 31 outliers final: 16 residues processed: 164 average time/residue: 0.2580 time to fit residues: 66.3598 Evaluate side-chains 150 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.0000 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 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 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15774 Z= 0.203 Angle : 0.572 9.460 21506 Z= 0.269 Chirality : 0.041 0.253 2550 Planarity : 0.004 0.045 2648 Dihedral : 9.255 108.039 2934 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.40 % Allowed : 13.01 % Favored : 84.59 % 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: -0.28 (0.20), residues: 1902 helix: 0.90 (0.16), residues: 1064 sheet: -2.23 (0.40), residues: 132 loop : -1.41 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1014 HIS 0.003 0.001 HIS A1253 PHE 0.016 0.001 PHE B 930 TYR 0.016 0.001 TYR A 646 ARG 0.003 0.000 ARG B 421 *********************** 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 187 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.7641 (m-80) cc_final: 0.7388 (m-10) REVERT: A 457 TRP cc_start: 0.6501 (t-100) cc_final: 0.5696 (t-100) REVERT: A 610 MET cc_start: 0.7980 (ttm) cc_final: 0.7663 (ptm) REVERT: A 707 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6447 (tp) REVERT: A 783 ASP cc_start: 0.7635 (t70) cc_final: 0.7367 (t0) REVERT: A 990 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 1011 TYR cc_start: 0.7831 (m-10) cc_final: 0.7370 (m-80) REVERT: A 1050 MET cc_start: 0.8908 (ttt) cc_final: 0.8220 (ttt) REVERT: A 1064 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6405 (mp0) REVERT: B 421 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7803 (mmm160) REVERT: B 422 TYR cc_start: 0.8728 (t80) cc_final: 0.8237 (t80) REVERT: B 457 TRP cc_start: 0.6079 (t-100) cc_final: 0.5394 (t-100) REVERT: B 579 TYR cc_start: 0.7640 (m-80) cc_final: 0.7117 (m-80) REVERT: B 607 MET cc_start: 0.8199 (mpp) cc_final: 0.7864 (mpp) REVERT: B 894 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: B 1064 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6465 (mp0) REVERT: B 1091 GLU cc_start: 0.6991 (pt0) cc_final: 0.6703 (tt0) outliers start: 39 outliers final: 20 residues processed: 172 average time/residue: 0.2352 time to fit residues: 63.7324 Evaluate side-chains 155 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 0.0020 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15774 Z= 0.155 Angle : 0.546 9.496 21506 Z= 0.256 Chirality : 0.040 0.220 2550 Planarity : 0.003 0.054 2648 Dihedral : 9.108 108.016 2934 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.59 % Allowed : 14.00 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1902 helix: 1.03 (0.16), residues: 1066 sheet: -2.16 (0.40), residues: 132 loop : -1.25 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1014 HIS 0.002 0.001 HIS A1253 PHE 0.015 0.001 PHE B 930 TYR 0.017 0.001 TYR B 886 ARG 0.006 0.000 ARG A 421 *********************** 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 181 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.7625 (m-80) cc_final: 0.7411 (m-10) REVERT: A 457 TRP cc_start: 0.6382 (t-100) cc_final: 0.5502 (t-100) REVERT: A 610 MET cc_start: 0.7993 (ttm) cc_final: 0.7618 (ptm) REVERT: A 990 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 1011 TYR cc_start: 0.7783 (m-10) cc_final: 0.7291 (m-80) REVERT: A 1050 MET cc_start: 0.8866 (ttt) cc_final: 0.8172 (ttt) REVERT: A 1064 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6414 (mp0) REVERT: B 421 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7557 (mmm160) REVERT: B 422 TYR cc_start: 0.8686 (t80) cc_final: 0.8192 (t80) REVERT: B 457 TRP cc_start: 0.6053 (t-100) cc_final: 0.5418 (t-100) REVERT: B 579 TYR cc_start: 0.7612 (m-80) cc_final: 0.7137 (m-80) REVERT: B 588 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: B 607 MET cc_start: 0.8101 (mpp) cc_final: 0.7586 (mpp) REVERT: B 616 MET cc_start: 0.8433 (ptt) cc_final: 0.8077 (ptm) REVERT: B 894 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 990 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8157 (mm) REVERT: B 1064 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6471 (mp0) REVERT: B 1091 GLU cc_start: 0.6934 (pt0) cc_final: 0.6647 (tt0) outliers start: 42 outliers final: 22 residues processed: 168 average time/residue: 0.2455 time to fit residues: 64.7584 Evaluate side-chains 157 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15774 Z= 0.200 Angle : 0.559 9.511 21506 Z= 0.264 Chirality : 0.040 0.219 2550 Planarity : 0.003 0.047 2648 Dihedral : 9.012 106.164 2934 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.51 % Allowed : 14.18 % Favored : 82.31 % 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: -0.05 (0.20), residues: 1902 helix: 1.03 (0.16), residues: 1066 sheet: -2.10 (0.41), residues: 132 loop : -1.22 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1014 HIS 0.003 0.001 HIS B1253 PHE 0.015 0.001 PHE A 791 TYR 0.015 0.001 TYR A 646 ARG 0.004 0.000 ARG A 693 *********************** 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 191 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: A 457 TRP cc_start: 0.6358 (t-100) cc_final: 0.5482 (t-100) REVERT: A 610 MET cc_start: 0.7992 (ttm) cc_final: 0.7611 (ptm) REVERT: A 664 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 990 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 994 MET cc_start: 0.7998 (mmm) cc_final: 0.7555 (tpt) REVERT: A 1011 TYR cc_start: 0.7751 (m-10) cc_final: 0.7159 (m-80) REVERT: A 1050 MET cc_start: 0.8951 (ttt) cc_final: 0.8430 (ttt) REVERT: A 1064 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6417 (mp0) REVERT: B 374 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: B 421 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7562 (mmm160) REVERT: B 422 TYR cc_start: 0.8673 (t80) cc_final: 0.8135 (t80) REVERT: B 457 TRP cc_start: 0.6053 (t-100) cc_final: 0.5408 (t-100) REVERT: B 579 TYR cc_start: 0.7614 (m-80) cc_final: 0.7128 (m-80) REVERT: B 766 MET cc_start: 0.7523 (mmt) cc_final: 0.7056 (mmt) REVERT: B 894 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: B 990 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 1050 MET cc_start: 0.8980 (ttt) cc_final: 0.8291 (ttt) REVERT: B 1091 GLU cc_start: 0.6848 (pt0) cc_final: 0.6573 (tt0) outliers start: 57 outliers final: 31 residues processed: 177 average time/residue: 0.2351 time to fit residues: 66.4003 Evaluate side-chains 170 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15774 Z= 0.194 Angle : 0.555 9.531 21506 Z= 0.263 Chirality : 0.040 0.221 2550 Planarity : 0.004 0.064 2648 Dihedral : 8.986 106.008 2934 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.21 % Allowed : 14.86 % Favored : 81.94 % 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: 0.01 (0.20), residues: 1902 helix: 1.06 (0.16), residues: 1066 sheet: -2.00 (0.42), residues: 132 loop : -1.16 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1014 HIS 0.003 0.001 HIS B1253 PHE 0.023 0.001 PHE A 853 TYR 0.016 0.001 TYR A 646 ARG 0.008 0.000 ARG A 421 *********************** 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 189 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: A 457 TRP cc_start: 0.6311 (t-100) cc_final: 0.5481 (t-100) REVERT: A 610 MET cc_start: 0.8021 (ttm) cc_final: 0.7578 (ttp) REVERT: A 664 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7721 (p) REVERT: A 990 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 1011 TYR cc_start: 0.7727 (m-10) cc_final: 0.7313 (m-80) REVERT: A 1064 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6459 (mp0) REVERT: B 374 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: B 421 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7559 (mmm160) REVERT: B 422 TYR cc_start: 0.8632 (t80) cc_final: 0.8091 (t80) REVERT: B 457 TRP cc_start: 0.6041 (t-100) cc_final: 0.5417 (t-100) REVERT: B 579 TYR cc_start: 0.7620 (m-80) cc_final: 0.7155 (m-80) REVERT: B 588 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: B 610 MET cc_start: 0.7861 (ttp) cc_final: 0.7641 (ptp) REVERT: B 664 SER cc_start: 0.7741 (OUTLIER) cc_final: 0.7472 (p) REVERT: B 707 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6477 (tt) REVERT: B 766 MET cc_start: 0.7698 (mmt) cc_final: 0.7405 (mmt) REVERT: B 990 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 1050 MET cc_start: 0.8974 (ttt) cc_final: 0.8312 (ttt) REVERT: B 1064 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6459 (mp0) REVERT: B 1091 GLU cc_start: 0.6810 (pt0) cc_final: 0.6518 (tt0) REVERT: B 1187 ARG cc_start: 0.6563 (ttt-90) cc_final: 0.6065 (tpt170) outliers start: 52 outliers final: 33 residues processed: 175 average time/residue: 0.2379 time to fit residues: 65.7591 Evaluate side-chains 173 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 616 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 0.0980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15774 Z= 0.142 Angle : 0.544 9.946 21506 Z= 0.256 Chirality : 0.039 0.222 2550 Planarity : 0.003 0.047 2648 Dihedral : 8.768 105.575 2934 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.34 % Allowed : 16.03 % Favored : 81.63 % 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: 0.18 (0.20), residues: 1902 helix: 1.19 (0.16), residues: 1066 sheet: -1.91 (0.42), residues: 132 loop : -1.08 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1014 HIS 0.002 0.000 HIS A1253 PHE 0.019 0.001 PHE A 853 TYR 0.016 0.001 TYR A 646 ARG 0.006 0.000 ARG A 421 *********************** 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 179 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: A 457 TRP cc_start: 0.6286 (t-100) cc_final: 0.5503 (t-100) REVERT: A 610 MET cc_start: 0.8037 (ttm) cc_final: 0.7600 (ttp) REVERT: A 664 SER cc_start: 0.7943 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 814 LYS cc_start: 0.6489 (mmtm) cc_final: 0.5956 (mttt) REVERT: A 990 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 1011 TYR cc_start: 0.7646 (m-10) cc_final: 0.7224 (m-80) REVERT: A 1064 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6474 (mp0) REVERT: B 374 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: B 421 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7551 (mmm160) REVERT: B 422 TYR cc_start: 0.8637 (t80) cc_final: 0.8059 (t80) REVERT: B 457 TRP cc_start: 0.5981 (t-100) cc_final: 0.5386 (t-100) REVERT: B 579 TYR cc_start: 0.7594 (m-80) cc_final: 0.7156 (m-80) REVERT: B 588 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: B 664 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 707 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (tt) REVERT: B 766 MET cc_start: 0.7625 (mmt) cc_final: 0.7348 (mmt) REVERT: B 990 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 1064 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6391 (mp0) REVERT: B 1091 GLU cc_start: 0.6730 (pt0) cc_final: 0.6456 (tt0) REVERT: B 1187 ARG cc_start: 0.6577 (ttt-90) cc_final: 0.6032 (tpt170) REVERT: B 1218 MET cc_start: 0.8155 (mmm) cc_final: 0.7868 (mmm) outliers start: 38 outliers final: 27 residues processed: 169 average time/residue: 0.2666 time to fit residues: 70.3512 Evaluate side-chains 171 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B1253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15774 Z= 0.391 Angle : 0.666 9.841 21506 Z= 0.321 Chirality : 0.044 0.222 2550 Planarity : 0.004 0.052 2648 Dihedral : 8.968 104.020 2934 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.90 % Allowed : 15.54 % 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: -0.32 (0.19), residues: 1902 helix: 0.77 (0.16), residues: 1078 sheet: -2.12 (0.42), residues: 132 loop : -1.31 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1014 HIS 0.004 0.001 HIS B1253 PHE 0.022 0.002 PHE A 791 TYR 0.013 0.001 TYR A1105 ARG 0.004 0.001 ARG B 693 *********************** 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 186 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: A 457 TRP cc_start: 0.6300 (t-100) cc_final: 0.5523 (t-100) REVERT: A 610 MET cc_start: 0.8027 (ttm) cc_final: 0.7631 (ttp) REVERT: A 664 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7753 (p) REVERT: A 766 MET cc_start: 0.8116 (mmt) cc_final: 0.7800 (mmt) REVERT: A 814 LYS cc_start: 0.6538 (mmtm) cc_final: 0.5934 (tppt) REVERT: A 990 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 1011 TYR cc_start: 0.7740 (m-10) cc_final: 0.7509 (m-80) REVERT: A 1064 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6543 (mp0) REVERT: B 374 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: B 421 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7502 (mmm160) REVERT: B 422 TYR cc_start: 0.8617 (t80) cc_final: 0.8023 (t80) REVERT: B 457 TRP cc_start: 0.6115 (t-100) cc_final: 0.5436 (t-100) REVERT: B 579 TYR cc_start: 0.7623 (m-80) cc_final: 0.7181 (m-80) REVERT: B 623 ASP cc_start: 0.7451 (t0) cc_final: 0.7049 (t0) REVERT: B 664 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 990 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 1050 MET cc_start: 0.9052 (ttt) cc_final: 0.8438 (ttt) REVERT: B 1064 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6496 (mp0) REVERT: B 1091 GLU cc_start: 0.6937 (pt0) cc_final: 0.6594 (tt0) outliers start: 47 outliers final: 34 residues processed: 174 average time/residue: 0.2359 time to fit residues: 64.3889 Evaluate side-chains 173 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15774 Z= 0.183 Angle : 0.574 11.266 21506 Z= 0.270 Chirality : 0.040 0.224 2550 Planarity : 0.003 0.048 2648 Dihedral : 8.725 103.945 2934 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.71 % Allowed : 15.97 % Favored : 81.32 % 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: -0.00 (0.20), residues: 1902 helix: 1.02 (0.16), residues: 1066 sheet: -1.99 (0.43), residues: 132 loop : -1.12 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1014 HIS 0.003 0.001 HIS A1053 PHE 0.013 0.001 PHE B 930 TYR 0.015 0.001 TYR A 646 ARG 0.004 0.000 ARG A 693 ********************** 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 180 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: A 457 TRP cc_start: 0.6208 (t-100) cc_final: 0.5401 (t-100) REVERT: A 610 MET cc_start: 0.8051 (ttm) cc_final: 0.7705 (ttp) REVERT: A 664 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 766 MET cc_start: 0.7946 (mmt) cc_final: 0.7392 (mmt) REVERT: A 814 LYS cc_start: 0.6495 (mmtm) cc_final: 0.5911 (tppt) REVERT: A 894 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: A 990 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 1064 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6502 (mp0) REVERT: B 374 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: B 421 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7498 (mmm160) REVERT: B 422 TYR cc_start: 0.8630 (t80) cc_final: 0.8041 (t80) REVERT: B 457 TRP cc_start: 0.6020 (t-100) cc_final: 0.5406 (t-100) REVERT: B 579 TYR cc_start: 0.7618 (m-80) cc_final: 0.7186 (m-80) REVERT: B 588 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: B 664 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7508 (p) REVERT: B 990 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8093 (mm) REVERT: B 1050 MET cc_start: 0.8930 (ttt) cc_final: 0.8360 (ttt) REVERT: B 1064 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6487 (mp0) REVERT: B 1091 GLU cc_start: 0.6840 (pt0) cc_final: 0.6516 (tt0) outliers start: 44 outliers final: 32 residues processed: 169 average time/residue: 0.2349 time to fit residues: 62.5978 Evaluate side-chains 170 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN A 496 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN B 496 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106259 restraints weight = 21171.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108337 restraints weight = 14077.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109804 restraints weight = 11043.085| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15774 Z= 0.194 Angle : 0.568 9.920 21506 Z= 0.267 Chirality : 0.040 0.222 2550 Planarity : 0.004 0.049 2648 Dihedral : 8.540 102.787 2934 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.47 % Allowed : 16.09 % Favored : 81.44 % 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: 0.07 (0.20), residues: 1902 helix: 1.06 (0.16), residues: 1066 sheet: -1.91 (0.42), residues: 132 loop : -1.08 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1014 HIS 0.002 0.001 HIS A1053 PHE 0.013 0.001 PHE A 791 TYR 0.015 0.001 TYR A 646 ARG 0.004 0.000 ARG B 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.78 seconds wall clock time: 49 minutes 8.07 seconds (2948.07 seconds total)