Starting phenix.real_space_refine on Fri Mar 15 12:00:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh6_12895/03_2024/7oh6_12895_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.027 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7470 2.51 5 N 1858 2.21 5 O 2167 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 359": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {' MG': 1, '2Y5': 1, 'ALF': 1, 'Q3G': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.11, per 1000 atoms: 0.53 Number of scatterers: 11552 At special positions: 0 Unit cell: (73.2152, 106.214, 174.273, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2167 8.00 N 1858 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.14 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=1, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 216 " " NAG D 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 10 sheets defined 40.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 190 through 196 removed outlier: 4.816A pdb=" N SER A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.125A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 249 through 280 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.848A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.202A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 removed outlier: 4.178A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 545 through 552 removed outlier: 5.396A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 632 Proline residue: A 621 - end of helix removed outlier: 3.836A pdb=" N ASN A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.507A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 5.512A pdb=" N GLU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 766 through 781 removed outlier: 3.655A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.554A pdb=" N GLU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 899 through 905 removed outlier: 4.071A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 931 through 943 removed outlier: 3.892A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 978 through 982 Processing helix chain 'A' and resid 990 through 1016 removed outlier: 3.936A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL A 999 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TRP A1003 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A1008 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1009 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR A1014 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1025 through 1028 No H-bonds generated for 'chain 'A' and resid 1025 through 1028' Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 4.505A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1091 through 1115 Processing helix chain 'A' and resid 1132 through 1153 removed outlier: 4.078A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1179 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1203 through 1230 Proline residue: A1213 - end of helix removed outlier: 5.055A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.536A pdb=" N TYR A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 removed outlier: 3.852A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix removed outlier: 3.783A pdb=" N THR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 174 through 179 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.715A pdb=" N ASN C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 195' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 331 through 356 Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 286 through 288 Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.988A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.881A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.258A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP A 898 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 861 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= G, first strand: chain 'A' and resid 687 through 690 removed outlier: 3.699A pdb=" N LYS A 673 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 678 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 671 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 680 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE A 669 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 570 through 577 removed outlier: 6.940A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.383A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 110 through 115 removed outlier: 4.497A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 5.12 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: 1862 1.31 - 1.44: 3208 1.44 - 1.56: 6655 1.56 - 1.69: 5 1.69 - 1.82: 81 Bond restraints: 11811 Sorted by residual: bond pdb=" F2 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.806 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.685 1.791 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" F4 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.686 1.790 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sigma weight residual 1.568 1.527 0.041 2.00e-02 2.50e+03 4.12e+00 ... (remaining 11806 not shown) Histogram of bond angle deviations from ideal: 89.28 - 107.34: 358 107.34 - 125.39: 15470 125.39 - 143.44: 171 143.44 - 161.49: 0 161.49 - 179.54: 2 Bond angle restraints: 16001 Sorted by residual: angle pdb=" F3 ALF A1502 " pdb="AL ALF A1502 " pdb=" F4 ALF A1502 " ideal model delta sigma weight residual 109.63 179.54 -69.91 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F1 ALF A1502 " pdb="AL ALF A1502 " pdb=" F2 ALF A1502 " ideal model delta sigma weight residual 108.68 177.97 -69.29 3.00e+00 1.11e-01 5.34e+02 angle pdb=" C21 2Y5 A1501 " pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " ideal model delta sigma weight residual 85.82 120.32 -34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " ideal model delta sigma weight residual 152.70 119.65 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " pdb=" C20 2Y5 A1501 " ideal model delta sigma weight residual 152.65 120.77 31.88 3.00e+00 1.11e-01 1.13e+02 ... (remaining 15996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.49: 6994 32.49 - 64.98: 107 64.98 - 97.47: 13 97.47 - 129.96: 5 129.96 - 162.45: 3 Dihedral angle restraints: 7122 sinusoidal: 2972 harmonic: 4150 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " pdb=" C27 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 329.24 166.79 162.45 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C1 2Y5 A1501 " pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 64.28 -150.43 -145.29 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1520 0.055 - 0.109: 259 0.109 - 0.164: 41 0.164 - 0.219: 1 0.219 - 0.273: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU A 693 " pdb=" CB LEU A 693 " pdb=" CD1 LEU A 693 " pdb=" CD2 LEU A 693 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE C 92 " pdb=" N ILE C 92 " pdb=" C ILE C 92 " pdb=" CB ILE C 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1819 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 746 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU A 746 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 746 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 747 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 621 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO A 621 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 621 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 622 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 745 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C HIS A 745 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS A 745 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 746 " 0.018 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 26 2.36 - 2.99: 6060 2.99 - 3.63: 16245 3.63 - 4.26: 25907 4.26 - 4.90: 43751 Nonbonded interactions: 91989 Sorted by model distance: nonbonded pdb=" F4 ALF A1502 " pdb="MG MG A1503 " model vdw 1.720 2.120 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1503 " model vdw 1.978 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1602 " model vdw 2.007 2.170 nonbonded pdb=" OD1 ASP A 954 " pdb="MG MG A1503 " model vdw 2.085 2.170 ... (remaining 91984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.090 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.003 0.121 11811 Z= 0.219 Angle : 1.132 69.913 16001 Z= 0.453 Chirality : 0.042 0.273 1822 Planarity : 0.005 0.060 1996 Dihedral : 12.693 162.448 4440 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 4.39 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1410 helix: -1.20 (0.20), residues: 587 sheet: -1.40 (0.34), residues: 202 loop : -2.10 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1132 HIS 0.006 0.001 HIS A 634 PHE 0.010 0.001 PHE C 317 TYR 0.012 0.001 TYR C 141 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8197 (tttt) cc_final: 0.7991 (mmpt) REVERT: A 277 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5872 (mmmt) REVERT: A 296 GLU cc_start: 0.7178 (tt0) cc_final: 0.6906 (tm-30) REVERT: A 437 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7733 (mtm180) REVERT: A 560 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6613 (p0) REVERT: A 637 ILE cc_start: 0.7819 (mt) cc_final: 0.7595 (mt) REVERT: A 866 ARG cc_start: 0.7197 (tmt170) cc_final: 0.6919 (tpt170) REVERT: A 1219 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.5667 (tpt90) REVERT: C 165 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7371 (mm-30) REVERT: C 168 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6728 (mmtt) outliers start: 15 outliers final: 4 residues processed: 210 average time/residue: 1.2265 time to fit residues: 278.6803 Evaluate side-chains 113 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1219 ARG Chi-restraints excluded: chain C residue 176 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 966 HIS A1242 GLN C 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11811 Z= 0.175 Angle : 0.566 11.688 16001 Z= 0.283 Chirality : 0.042 0.240 1822 Planarity : 0.004 0.046 1996 Dihedral : 11.616 159.419 1744 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 2.31 % Allowed : 11.81 % Favored : 85.87 % 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: -1.62 (0.22), residues: 1410 helix: -0.33 (0.22), residues: 589 sheet: -1.01 (0.34), residues: 205 loop : -1.77 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1172 HIS 0.005 0.001 HIS A 634 PHE 0.011 0.001 PHE A 495 TYR 0.020 0.001 TYR C 77 ARG 0.005 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8247 (tttt) cc_final: 0.7972 (mmpt) REVERT: A 241 HIS cc_start: 0.6513 (m90) cc_final: 0.5634 (p90) REVERT: A 277 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5816 (mmmt) REVERT: A 296 GLU cc_start: 0.7164 (tt0) cc_final: 0.6954 (tm-30) REVERT: A 336 THR cc_start: 0.7583 (p) cc_final: 0.7232 (t) REVERT: A 386 MET cc_start: 0.6832 (ttp) cc_final: 0.6592 (ttm) REVERT: A 437 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7708 (mtm180) REVERT: A 690 TYR cc_start: 0.5938 (m-80) cc_final: 0.5552 (m-80) REVERT: A 691 GLN cc_start: 0.7079 (mm110) cc_final: 0.6298 (tm-30) REVERT: A 738 TYR cc_start: 0.6396 (m-10) cc_final: 0.6137 (m-10) REVERT: A 761 MET cc_start: 0.6138 (tmm) cc_final: 0.5884 (tmm) REVERT: A 915 LEU cc_start: 0.8056 (tp) cc_final: 0.7830 (tp) REVERT: A 1219 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.5613 (tpt90) REVERT: C 143 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8636 (mm) REVERT: C 165 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7353 (mm-30) outliers start: 29 outliers final: 15 residues processed: 135 average time/residue: 1.1301 time to fit residues: 167.0843 Evaluate side-chains 114 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 492 PHE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1219 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11811 Z= 0.156 Angle : 0.537 12.387 16001 Z= 0.267 Chirality : 0.042 0.221 1822 Planarity : 0.004 0.045 1996 Dihedral : 10.458 149.449 1742 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.03 % Allowed : 12.29 % Favored : 84.68 % 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: -1.17 (0.22), residues: 1410 helix: 0.08 (0.22), residues: 589 sheet: -0.71 (0.35), residues: 201 loop : -1.60 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.013 0.001 PHE A 492 TYR 0.018 0.001 TYR C 77 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8255 (tttt) cc_final: 0.7987 (mmpt) REVERT: A 241 HIS cc_start: 0.6499 (m90) cc_final: 0.5604 (p90) REVERT: A 263 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.6231 (tmm) REVERT: A 277 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5789 (mmmt) REVERT: A 296 GLU cc_start: 0.7172 (tt0) cc_final: 0.6942 (tm-30) REVERT: A 336 THR cc_start: 0.7598 (p) cc_final: 0.7368 (t) REVERT: A 400 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8446 (ttt) REVERT: A 435 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 690 TYR cc_start: 0.5856 (m-80) cc_final: 0.5519 (m-80) REVERT: A 691 GLN cc_start: 0.7112 (mm110) cc_final: 0.6371 (tm-30) REVERT: A 698 PHE cc_start: 0.6233 (t80) cc_final: 0.6006 (t80) REVERT: A 705 MET cc_start: 0.6287 (tpp) cc_final: 0.5790 (ttm) REVERT: A 738 TYR cc_start: 0.6722 (m-10) cc_final: 0.6415 (m-10) REVERT: A 761 MET cc_start: 0.6371 (tmm) cc_final: 0.6145 (tmm) REVERT: A 1228 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7640 (tmt170) REVERT: C 165 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7363 (mm-30) REVERT: C 310 LEU cc_start: 0.7441 (tp) cc_final: 0.7199 (tp) outliers start: 38 outliers final: 19 residues processed: 129 average time/residue: 1.0123 time to fit residues: 144.5876 Evaluate side-chains 119 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0170 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11811 Z= 0.139 Angle : 0.510 11.835 16001 Z= 0.253 Chirality : 0.041 0.225 1822 Planarity : 0.004 0.044 1996 Dihedral : 9.539 155.069 1738 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 3.35 % Allowed : 13.25 % Favored : 83.40 % 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: -0.85 (0.23), residues: 1410 helix: 0.35 (0.23), residues: 592 sheet: -0.61 (0.35), residues: 211 loop : -1.41 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.011 0.001 PHE A1048 TYR 0.017 0.001 TYR C 77 ARG 0.006 0.000 ARG A 981 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8232 (tttt) cc_final: 0.7956 (mmpt) REVERT: A 241 HIS cc_start: 0.6476 (m90) cc_final: 0.5689 (p90) REVERT: A 263 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6191 (tmm) REVERT: A 277 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5754 (mmmt) REVERT: A 296 GLU cc_start: 0.7162 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 400 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8307 (ttt) REVERT: A 435 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8214 (pp) REVERT: A 690 TYR cc_start: 0.5960 (m-80) cc_final: 0.5566 (m-80) REVERT: A 691 GLN cc_start: 0.7175 (mm110) cc_final: 0.6451 (tm-30) REVERT: A 698 PHE cc_start: 0.6230 (t80) cc_final: 0.5978 (t80) REVERT: A 705 MET cc_start: 0.6156 (tpp) cc_final: 0.5820 (ttm) REVERT: A 738 TYR cc_start: 0.6774 (m-10) cc_final: 0.6410 (m-10) REVERT: A 761 MET cc_start: 0.6288 (tmm) cc_final: 0.6049 (tmm) REVERT: C 165 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7392 (mm-30) REVERT: C 310 LEU cc_start: 0.7445 (tp) cc_final: 0.7146 (tp) outliers start: 42 outliers final: 18 residues processed: 130 average time/residue: 0.9162 time to fit residues: 133.0325 Evaluate side-chains 119 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.0050 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11811 Z= 0.299 Angle : 0.597 12.399 16001 Z= 0.300 Chirality : 0.045 0.208 1822 Planarity : 0.004 0.043 1996 Dihedral : 9.247 154.554 1736 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 4.23 % Allowed : 14.13 % Favored : 81.64 % 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: -0.99 (0.22), residues: 1410 helix: 0.27 (0.22), residues: 584 sheet: -0.68 (0.35), residues: 205 loop : -1.52 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1172 HIS 0.005 0.001 HIS C 150 PHE 0.019 0.002 PHE A 492 TYR 0.016 0.002 TYR C 141 ARG 0.004 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 99 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8304 (tttt) cc_final: 0.7995 (mmpt) REVERT: A 241 HIS cc_start: 0.6493 (m90) cc_final: 0.5746 (p90) REVERT: A 263 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.6234 (tmm) REVERT: A 277 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5955 (mmmt) REVERT: A 296 GLU cc_start: 0.7188 (tt0) cc_final: 0.6853 (tm-30) REVERT: A 400 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8275 (ttt) REVERT: A 435 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 690 TYR cc_start: 0.5966 (m-80) cc_final: 0.5557 (m-80) REVERT: A 691 GLN cc_start: 0.7172 (mm110) cc_final: 0.6332 (tm-30) REVERT: A 738 TYR cc_start: 0.6694 (m-10) cc_final: 0.6354 (m-10) REVERT: A 761 MET cc_start: 0.6055 (tmm) cc_final: 0.5805 (tmm) REVERT: A 864 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 1228 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7791 (tmt170) REVERT: C 165 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7332 (mm-30) REVERT: C 330 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5130 (mmm) outliers start: 53 outliers final: 25 residues processed: 132 average time/residue: 1.0155 time to fit residues: 148.9139 Evaluate side-chains 120 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 330 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11811 Z= 0.162 Angle : 0.554 12.679 16001 Z= 0.274 Chirality : 0.042 0.226 1822 Planarity : 0.004 0.041 1996 Dihedral : 8.854 155.007 1736 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 3.11 % Allowed : 15.48 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1410 helix: 0.45 (0.23), residues: 593 sheet: -0.54 (0.35), residues: 209 loop : -1.36 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1172 HIS 0.003 0.001 HIS A 745 PHE 0.011 0.001 PHE A1048 TYR 0.016 0.001 TYR C 77 ARG 0.007 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 97 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8282 (tttt) cc_final: 0.7974 (mmpt) REVERT: A 241 HIS cc_start: 0.6471 (m90) cc_final: 0.5725 (p90) REVERT: A 263 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6262 (tmm) REVERT: A 277 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5814 (mmmt) REVERT: A 296 GLU cc_start: 0.7160 (tt0) cc_final: 0.6893 (tm-30) REVERT: A 400 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (ttt) REVERT: A 435 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 690 TYR cc_start: 0.5928 (m-80) cc_final: 0.5508 (m-80) REVERT: A 691 GLN cc_start: 0.7180 (mm110) cc_final: 0.6465 (tm-30) REVERT: A 705 MET cc_start: 0.6247 (tpp) cc_final: 0.5767 (ttm) REVERT: A 738 TYR cc_start: 0.6658 (m-10) cc_final: 0.6304 (m-10) REVERT: A 761 MET cc_start: 0.6069 (tmm) cc_final: 0.5816 (tmm) REVERT: A 864 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 1228 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7728 (tmt170) REVERT: C 165 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7361 (mm-30) outliers start: 39 outliers final: 26 residues processed: 121 average time/residue: 1.0340 time to fit residues: 138.0212 Evaluate side-chains 120 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.0670 chunk 77 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11811 Z= 0.135 Angle : 0.539 12.472 16001 Z= 0.265 Chirality : 0.041 0.213 1822 Planarity : 0.004 0.041 1996 Dihedral : 8.571 155.058 1735 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 2.79 % Allowed : 16.20 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1410 helix: 0.66 (0.23), residues: 585 sheet: -0.37 (0.35), residues: 209 loop : -1.28 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.015 0.001 PHE A 492 TYR 0.015 0.001 TYR C 77 ARG 0.010 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8193 (tttt) cc_final: 0.7929 (mmpt) REVERT: A 241 HIS cc_start: 0.6415 (m90) cc_final: 0.5732 (p90) REVERT: A 263 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6221 (tmm) REVERT: A 277 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5717 (mmmt) REVERT: A 296 GLU cc_start: 0.7150 (tt0) cc_final: 0.6891 (tm-30) REVERT: A 400 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8243 (ttt) REVERT: A 435 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8239 (pp) REVERT: A 690 TYR cc_start: 0.5906 (m-80) cc_final: 0.5467 (m-80) REVERT: A 691 GLN cc_start: 0.7194 (mm110) cc_final: 0.6315 (tm-30) REVERT: A 738 TYR cc_start: 0.6678 (m-10) cc_final: 0.6332 (m-10) REVERT: A 761 MET cc_start: 0.6171 (tmm) cc_final: 0.5956 (tmm) REVERT: A 864 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 1228 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7625 (tmt170) REVERT: C 165 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7383 (mm-30) REVERT: C 310 LEU cc_start: 0.7405 (tp) cc_final: 0.7132 (tp) outliers start: 35 outliers final: 17 residues processed: 125 average time/residue: 1.0170 time to fit residues: 142.2025 Evaluate side-chains 116 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11811 Z= 0.213 Angle : 0.573 12.879 16001 Z= 0.283 Chirality : 0.043 0.242 1822 Planarity : 0.004 0.047 1996 Dihedral : 8.577 154.768 1735 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.19 % Allowed : 16.28 % Favored : 80.53 % 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: -0.54 (0.23), residues: 1410 helix: 0.66 (0.23), residues: 578 sheet: -0.36 (0.35), residues: 206 loop : -1.30 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.019 0.001 PHE A 709 TYR 0.013 0.001 TYR C 141 ARG 0.006 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 96 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8232 (tttt) cc_final: 0.7962 (mmpt) REVERT: A 241 HIS cc_start: 0.6437 (m90) cc_final: 0.5757 (p90) REVERT: A 263 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: A 277 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5710 (mmmt) REVERT: A 296 GLU cc_start: 0.7175 (tt0) cc_final: 0.6887 (tm-30) REVERT: A 400 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8196 (ttt) REVERT: A 435 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 690 TYR cc_start: 0.5824 (m-80) cc_final: 0.5426 (m-80) REVERT: A 691 GLN cc_start: 0.7197 (mm110) cc_final: 0.6369 (tm-30) REVERT: A 738 TYR cc_start: 0.6869 (m-10) cc_final: 0.6549 (m-10) REVERT: A 864 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 165 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7348 (mm-30) outliers start: 40 outliers final: 22 residues processed: 123 average time/residue: 1.0145 time to fit residues: 138.5179 Evaluate side-chains 116 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 710 ARG Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11811 Z= 0.168 Angle : 0.570 12.432 16001 Z= 0.281 Chirality : 0.042 0.240 1822 Planarity : 0.004 0.043 1996 Dihedral : 8.506 154.623 1735 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 2.23 % Allowed : 17.72 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1410 helix: 0.76 (0.23), residues: 574 sheet: -0.29 (0.36), residues: 204 loop : -1.26 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.017 0.001 PHE A 492 TYR 0.014 0.001 TYR C 77 ARG 0.007 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8163 (tttt) cc_final: 0.7902 (mmpt) REVERT: A 241 HIS cc_start: 0.6502 (m90) cc_final: 0.5803 (p90) REVERT: A 263 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6284 (tmm) REVERT: A 277 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5710 (mmmt) REVERT: A 296 GLU cc_start: 0.7162 (tt0) cc_final: 0.6887 (tm-30) REVERT: A 400 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8189 (ttt) REVERT: A 435 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (pp) REVERT: A 652 SER cc_start: 0.7364 (t) cc_final: 0.6734 (p) REVERT: A 690 TYR cc_start: 0.5909 (m-80) cc_final: 0.5517 (m-80) REVERT: A 691 GLN cc_start: 0.7244 (mm110) cc_final: 0.6483 (tm-30) REVERT: A 738 TYR cc_start: 0.6830 (m-10) cc_final: 0.6533 (m-10) REVERT: A 761 MET cc_start: 0.6196 (tmm) cc_final: 0.5993 (tmm) REVERT: A 864 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 165 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7366 (mm-30) outliers start: 28 outliers final: 17 residues processed: 106 average time/residue: 0.9667 time to fit residues: 114.6018 Evaluate side-chains 107 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 0.0270 chunk 140 optimal weight: 0.0000 chunk 129 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11811 Z= 0.176 Angle : 0.577 12.424 16001 Z= 0.285 Chirality : 0.042 0.262 1822 Planarity : 0.004 0.042 1996 Dihedral : 8.431 154.471 1735 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 1.76 % Allowed : 18.12 % Favored : 80.13 % 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: -0.44 (0.23), residues: 1410 helix: 0.77 (0.23), residues: 574 sheet: -0.32 (0.36), residues: 204 loop : -1.25 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1172 HIS 0.003 0.001 HIS A 634 PHE 0.022 0.001 PHE A1048 TYR 0.013 0.001 TYR C 77 ARG 0.006 0.000 ARG A 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8172 (tttt) cc_final: 0.7908 (mmpt) REVERT: A 241 HIS cc_start: 0.6573 (m90) cc_final: 0.5834 (p90) REVERT: A 263 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.6212 (tmm) REVERT: A 277 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5689 (mmmt) REVERT: A 400 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8175 (ttt) REVERT: A 435 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8203 (pp) REVERT: A 652 SER cc_start: 0.7402 (t) cc_final: 0.6772 (p) REVERT: A 690 TYR cc_start: 0.5980 (m-80) cc_final: 0.5556 (m-80) REVERT: A 691 GLN cc_start: 0.7192 (mm110) cc_final: 0.6477 (tm-30) REVERT: A 738 TYR cc_start: 0.6805 (m-10) cc_final: 0.6506 (m-10) REVERT: A 864 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7617 (mm-30) REVERT: C 54 CYS cc_start: 0.7735 (t) cc_final: 0.7299 (t) REVERT: C 165 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7345 (mm-30) outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 0.9671 time to fit residues: 115.4686 Evaluate side-chains 112 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 98 optimal weight: 0.0050 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104635 restraints weight = 16177.382| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.65 r_work: 0.3460 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11811 Z= 0.235 Angle : 0.602 12.457 16001 Z= 0.298 Chirality : 0.044 0.239 1822 Planarity : 0.004 0.041 1996 Dihedral : 8.493 154.384 1735 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 18.12 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1410 helix: 0.70 (0.23), residues: 568 sheet: -0.41 (0.36), residues: 205 loop : -1.31 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1172 HIS 0.003 0.001 HIS C 150 PHE 0.022 0.001 PHE A 492 TYR 0.014 0.001 TYR C 141 ARG 0.006 0.000 ARG A 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.77 seconds wall clock time: 66 minutes 17.61 seconds (3977.61 seconds total)