Starting phenix.real_space_refine on Sun Apr 7 21:27:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ox9_17261/04_2024/8ox9_17261_updated.pdb" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 P 5 5.49 5 Mg 1 5.21 5 S 57 5.16 5 Be 1 3.05 5 C 7464 2.51 5 N 1915 2.21 5 O 2136 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11582 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8765 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 26, 'TRANS': 1057} Chain breaks: 3 Chain: "B" Number of atoms: 2633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2633 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 25, 'TRANS': 301} Chain: "C" 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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {' MG': 1, 'BEF': 1, 'IP9': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 6.53, per 1000 atoms: 0.56 Number of scatterers: 11582 At special positions: 0 Unit cell: (90.0624, 97.3088, 175.984, 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 57 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2136 8.00 N 1915 7.00 C 7464 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.3 seconds 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 10 sheets defined 44.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 145 through 174 removed outlier: 3.541A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 171 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.744A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 332 through 365 removed outlier: 3.815A pdb=" N GLN A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.040A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.797A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.757A pdb=" N LEU A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.585A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 663 through 678 removed outlier: 3.812A pdb=" N LYS A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 758 through 772 Processing helix chain 'A' and resid 803 through 809 removed outlier: 3.621A pdb=" N GLU A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 859 removed outlier: 3.704A pdb=" N LYS A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 840 " --> pdb=" O THR A 836 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 883 Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.674A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 900 " --> pdb=" O ASP A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 929 through 937 removed outlier: 3.773A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 936 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 971 removed outlier: 3.570A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 4.025A pdb=" N THR A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1003 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1016 through 1023 Processing helix chain 'A' and resid 1030 through 1055 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.563A pdb=" N ILE A1076 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1115 removed outlier: 4.287A pdb=" N PHE A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1124 Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 4.585A pdb=" N ARG A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1170 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1174 through 1180 Processing helix chain 'B' and resid 47 through 74 Proline residue: B 52 - end of helix removed outlier: 3.655A pdb=" N ILE B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.783A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 150 No H-bonds generated for 'chain 'B' and resid 147 through 150' Processing helix chain 'B' and resid 155 through 160 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 323 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.995A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.742A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 309 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 214 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.856A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 924 through 926 removed outlier: 6.262A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR A 732 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS A 865 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 862 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.554A pdb=" N LYS A 468 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 614 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 604 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.750A pdb=" N MET A 538 " --> pdb=" O GLN A 549 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 567 through 569 Processing sheet with id= H, first strand: chain 'A' and resid 460 through 466 removed outlier: 7.367A pdb=" N LYS A 709 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 463 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 707 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 77 through 81 removed outlier: 5.852A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 102 through 109 removed outlier: 4.149A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1320 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: 3.99 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: 1847 1.31 - 1.43: 3287 1.43 - 1.56: 6609 1.56 - 1.69: 8 1.69 - 1.81: 88 Bond restraints: 11839 Sorted by residual: bond pdb=" BE BEF A1301 " pdb=" F2 BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C31 POV A1303 " pdb=" O31 POV A1303 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C21 POV A1303 " pdb=" O21 POV A1303 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" BE BEF A1301 " pdb=" F1 BEF A1301 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 11834 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 322 107.23 - 113.91: 6650 113.91 - 120.60: 4865 120.60 - 127.28: 4072 127.28 - 133.96: 124 Bond angle restraints: 16033 Sorted by residual: angle pdb=" O11 POV A1303 " pdb=" P POV A1303 " pdb=" O12 POV A1303 " ideal model delta sigma weight residual 97.67 110.59 -12.92 3.00e+00 1.11e-01 1.86e+01 angle pdb=" F2 BEF A1301 " pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.93 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O13 POV A1303 " pdb=" P POV A1303 " pdb=" O14 POV A1303 " ideal model delta sigma weight residual 121.11 109.77 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C2 IP9 A1304 " pdb=" C1 IP9 A1304 " pdb=" C6 IP9 A1304 " ideal model delta sigma weight residual 112.08 123.11 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" F1 BEF A1301 " pdb=" BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 120.12 110.24 9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.11: 6743 25.11 - 50.22: 318 50.22 - 75.33: 29 75.33 - 100.45: 14 100.45 - 125.56: 6 Dihedral angle restraints: 7110 sinusoidal: 2976 harmonic: 4134 Sorted by residual: dihedral pdb=" CA ASN A1029 " pdb=" C ASN A1029 " pdb=" N TYR A1030 " pdb=" CA TYR A1030 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C3 IP9 A1304 " pdb=" C4 IP9 A1304 " pdb=" C5 IP9 A1304 " pdb=" C6 IP9 A1304 " ideal model delta sinusoidal sigma weight residual -52.96 72.60 -125.56 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CA MET A1114 " pdb=" C MET A1114 " pdb=" N PHE A1115 " pdb=" CA PHE A1115 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 1788 0.384 - 0.769: 0 0.769 - 1.153: 0 1.153 - 1.537: 0 1.537 - 1.921: 1 Chirality restraints: 1789 Sorted by residual: chirality pdb=" C1 IP9 A1304 " pdb=" C2 IP9 A1304 " pdb=" C6 IP9 A1304 " pdb=" O1 IP9 A1304 " both_signs ideal model delta sigma weight residual False -2.50 -0.58 -1.92 2.00e-01 2.50e+01 9.23e+01 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 NAG B 402 " pdb=" C1 NAG B 402 " pdb=" C3 NAG B 402 " pdb=" N2 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.49 -2.35 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1786 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 51 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 52 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO A 109 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " 0.034 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 170 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.029 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 56 2.41 - 3.03: 7105 3.03 - 3.65: 17571 3.65 - 4.28: 28093 4.28 - 4.90: 46834 Nonbonded interactions: 99659 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" F2 BEF A1301 " model vdw 1.787 2.390 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.944 2.440 nonbonded pdb=" OG1 THR A 343 " pdb=" OH TYR A1030 " model vdw 1.977 2.440 nonbonded pdb=" OG1 THR A 155 " pdb=" O HOH A1401 " model vdw 2.040 2.440 nonbonded pdb=" OG SER A 218 " pdb=" OD1 ASP A 304 " model vdw 2.043 2.440 ... (remaining 99654 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=0.00 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: 0.630 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: 3.490 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.004 0.084 11839 Z= 0.242 Angle : 0.612 12.922 16033 Z= 0.284 Chirality : 0.061 1.921 1789 Planarity : 0.004 0.053 2013 Dihedral : 14.920 125.556 4437 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.10 (0.23), residues: 1401 helix: 0.27 (0.22), residues: 608 sheet: 0.78 (0.37), residues: 194 loop : -0.24 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 983 HIS 0.002 0.001 HIS A 307 PHE 0.015 0.001 PHE A 926 TYR 0.008 0.001 TYR B 122 ARG 0.004 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.231 Fit side-chains REVERT: A 735 LYS cc_start: 0.8382 (ptmm) cc_final: 0.8006 (ptmm) REVERT: A 766 HIS cc_start: 0.7543 (t-90) cc_final: 0.7272 (t70) REVERT: B 117 ASN cc_start: 0.8705 (m110) cc_final: 0.8502 (m-40) REVERT: B 338 LEU cc_start: 0.7572 (tp) cc_final: 0.7371 (tp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 1.4025 time to fit residues: 213.8047 Evaluate side-chains 100 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.0010 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 HIS A1179 GLN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN B 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11839 Z= 0.191 Angle : 0.560 9.385 16033 Z= 0.283 Chirality : 0.042 0.246 1789 Planarity : 0.004 0.044 2013 Dihedral : 9.763 117.994 1713 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 1.21 % Allowed : 7.66 % Favored : 91.14 % 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: 1401 helix: 0.62 (0.21), residues: 622 sheet: 0.83 (0.36), residues: 195 loop : -0.11 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.015 0.001 PHE A 926 TYR 0.013 0.001 TYR A 511 ARG 0.009 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.280 Fit side-chains REVERT: A 603 MET cc_start: 0.6610 (ppp) cc_final: 0.6085 (tmt) REVERT: A 766 HIS cc_start: 0.7453 (t-90) cc_final: 0.7085 (t70) REVERT: A 845 LYS cc_start: 0.7557 (pttm) cc_final: 0.7328 (ptpp) REVERT: A 1055 TYR cc_start: 0.8555 (m-80) cc_final: 0.8295 (m-80) REVERT: B 338 LEU cc_start: 0.7862 (tp) cc_final: 0.7514 (mt) outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 1.2296 time to fit residues: 162.3385 Evaluate side-chains 106 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain B residue 166 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 102 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1179 GLN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11839 Z= 0.170 Angle : 0.511 9.472 16033 Z= 0.257 Chirality : 0.041 0.257 1789 Planarity : 0.003 0.052 2013 Dihedral : 8.727 115.281 1713 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 9.67 % Favored : 88.40 % 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: 0.67 (0.23), residues: 1401 helix: 0.94 (0.21), residues: 621 sheet: 0.91 (0.36), residues: 197 loop : -0.13 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.014 0.001 PHE A 926 TYR 0.015 0.001 TYR A 123 ARG 0.008 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.364 Fit side-chains REVERT: A 735 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8005 (ptmm) REVERT: A 1055 TYR cc_start: 0.8575 (m-80) cc_final: 0.8346 (m-80) REVERT: A 1114 MET cc_start: 0.7218 (mtm) cc_final: 0.7002 (mtt) REVERT: B 225 GLU cc_start: 0.7715 (mp0) cc_final: 0.7469 (pm20) REVERT: B 338 LEU cc_start: 0.7906 (tp) cc_final: 0.7582 (mt) outliers start: 24 outliers final: 12 residues processed: 118 average time/residue: 1.1843 time to fit residues: 153.4162 Evaluate side-chains 109 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.0060 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1179 GLN B 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11839 Z= 0.172 Angle : 0.506 9.565 16033 Z= 0.253 Chirality : 0.041 0.258 1789 Planarity : 0.003 0.050 2013 Dihedral : 8.336 112.860 1713 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 2.01 % Allowed : 11.44 % Favored : 86.54 % 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: 0.76 (0.23), residues: 1401 helix: 1.04 (0.21), residues: 627 sheet: 0.93 (0.36), residues: 197 loop : -0.13 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE A 926 TYR 0.014 0.001 TYR A 123 ARG 0.011 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.355 Fit side-chains REVERT: A 465 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (p) REVERT: A 1055 TYR cc_start: 0.8583 (m-80) cc_final: 0.8335 (m-80) REVERT: A 1114 MET cc_start: 0.7282 (mtm) cc_final: 0.7059 (mtt) REVERT: B 338 LEU cc_start: 0.7906 (tp) cc_final: 0.7609 (mt) outliers start: 25 outliers final: 12 residues processed: 119 average time/residue: 1.1851 time to fit residues: 154.7945 Evaluate side-chains 114 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 166 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 36 GLN B 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11839 Z= 0.270 Angle : 0.549 9.527 16033 Z= 0.275 Chirality : 0.043 0.255 1789 Planarity : 0.004 0.059 2013 Dihedral : 8.342 112.864 1713 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.42 % Allowed : 12.25 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1401 helix: 1.01 (0.21), residues: 625 sheet: 0.91 (0.35), residues: 197 loop : -0.17 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.016 0.002 PHE A 955 TYR 0.015 0.001 TYR A 123 ARG 0.014 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.383 Fit side-chains REVERT: A 172 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 1055 TYR cc_start: 0.8610 (m-80) cc_final: 0.8307 (m-80) REVERT: A 1114 MET cc_start: 0.7406 (mtm) cc_final: 0.7206 (mtt) REVERT: B 338 LEU cc_start: 0.7885 (tp) cc_final: 0.7555 (mt) outliers start: 30 outliers final: 19 residues processed: 123 average time/residue: 1.1736 time to fit residues: 158.2706 Evaluate side-chains 121 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN B 254 ASN B 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11839 Z= 0.360 Angle : 0.590 9.472 16033 Z= 0.294 Chirality : 0.045 0.250 1789 Planarity : 0.004 0.066 2013 Dihedral : 8.517 113.585 1713 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.66 % Allowed : 13.13 % Favored : 84.21 % 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: 1401 helix: 0.81 (0.21), residues: 626 sheet: 0.96 (0.36), residues: 191 loop : -0.22 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.018 0.002 PHE A 955 TYR 0.015 0.002 TYR A 123 ARG 0.015 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.330 Fit side-chains REVERT: A 603 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6519 (tmt) REVERT: A 1055 TYR cc_start: 0.8591 (m-80) cc_final: 0.8335 (m-80) REVERT: B 338 LEU cc_start: 0.7858 (tp) cc_final: 0.7480 (mt) outliers start: 33 outliers final: 20 residues processed: 123 average time/residue: 1.1611 time to fit residues: 157.0148 Evaluate side-chains 121 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 916 MET Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11839 Z= 0.190 Angle : 0.521 10.982 16033 Z= 0.261 Chirality : 0.041 0.252 1789 Planarity : 0.004 0.069 2013 Dihedral : 8.291 111.631 1713 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.18 % Allowed : 14.18 % Favored : 83.64 % 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: 0.75 (0.23), residues: 1401 helix: 1.07 (0.21), residues: 619 sheet: 0.84 (0.35), residues: 201 loop : -0.14 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.000 HIS A 417 PHE 0.014 0.001 PHE A 955 TYR 0.014 0.001 TYR A 123 ARG 0.016 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.349 Fit side-chains REVERT: A 465 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 603 MET cc_start: 0.6826 (ppp) cc_final: 0.6470 (tmt) REVERT: B 225 GLU cc_start: 0.7849 (mp0) cc_final: 0.7464 (pm20) REVERT: B 338 LEU cc_start: 0.7827 (tp) cc_final: 0.7498 (mt) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 1.1263 time to fit residues: 151.4728 Evaluate side-chains 118 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 chunk 129 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11839 Z= 0.167 Angle : 0.518 11.715 16033 Z= 0.257 Chirality : 0.041 0.254 1789 Planarity : 0.003 0.067 2013 Dihedral : 8.133 110.441 1713 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.01 % Allowed : 14.59 % 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: 0.89 (0.23), residues: 1401 helix: 1.16 (0.21), residues: 620 sheet: 0.97 (0.35), residues: 195 loop : -0.06 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.000 HIS A 417 PHE 0.013 0.001 PHE A 955 TYR 0.017 0.001 TYR A 476 ARG 0.017 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.383 Fit side-chains REVERT: A 169 MET cc_start: 0.8087 (mtp) cc_final: 0.7882 (mtp) REVERT: A 603 MET cc_start: 0.6901 (ppp) cc_final: 0.6547 (tmt) REVERT: B 225 GLU cc_start: 0.7825 (mp0) cc_final: 0.7452 (pm20) REVERT: B 338 LEU cc_start: 0.7870 (tp) cc_final: 0.7589 (mt) outliers start: 25 outliers final: 18 residues processed: 123 average time/residue: 1.1530 time to fit residues: 156.6100 Evaluate side-chains 120 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 254 ASN B 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11839 Z= 0.190 Angle : 0.531 12.122 16033 Z= 0.261 Chirality : 0.041 0.255 1789 Planarity : 0.004 0.078 2013 Dihedral : 8.092 110.154 1713 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 1.85 % Allowed : 15.15 % Favored : 83.00 % 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: 0.89 (0.23), residues: 1401 helix: 1.12 (0.21), residues: 627 sheet: 0.96 (0.35), residues: 195 loop : -0.00 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.000 HIS A 417 PHE 0.014 0.001 PHE A 955 TYR 0.017 0.001 TYR A 476 ARG 0.019 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.331 Fit side-chains REVERT: A 530 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5508 (tt) REVERT: A 603 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6729 (tmt) REVERT: A 674 MET cc_start: 0.2601 (mmp) cc_final: 0.2209 (mmt) REVERT: B 225 GLU cc_start: 0.7806 (mp0) cc_final: 0.7444 (pm20) REVERT: B 338 LEU cc_start: 0.7854 (tp) cc_final: 0.7589 (mt) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 1.0647 time to fit residues: 147.7716 Evaluate side-chains 121 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11839 Z= 0.189 Angle : 0.528 12.154 16033 Z= 0.260 Chirality : 0.041 0.254 1789 Planarity : 0.004 0.086 2013 Dihedral : 8.060 109.754 1713 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 1.53 % Allowed : 15.79 % Favored : 82.68 % 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: 0.90 (0.23), residues: 1401 helix: 1.16 (0.22), residues: 620 sheet: 0.94 (0.35), residues: 195 loop : -0.01 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.014 0.001 PHE B 108 TYR 0.018 0.001 TYR A 476 ARG 0.019 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 1.355 Fit side-chains REVERT: A 530 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5522 (tt) REVERT: A 603 MET cc_start: 0.7156 (ppp) cc_final: 0.6816 (tmt) REVERT: A 674 MET cc_start: 0.2567 (mmp) cc_final: 0.2198 (mmt) REVERT: B 225 GLU cc_start: 0.7771 (mp0) cc_final: 0.7427 (pm20) REVERT: B 338 LEU cc_start: 0.7851 (tp) cc_final: 0.7594 (mt) outliers start: 19 outliers final: 16 residues processed: 120 average time/residue: 1.1296 time to fit residues: 149.1082 Evaluate side-chains 120 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN B 302 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116073 restraints weight = 12732.628| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.24 r_work: 0.3407 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11839 Z= 0.182 Angle : 0.530 11.960 16033 Z= 0.261 Chirality : 0.041 0.253 1789 Planarity : 0.004 0.084 2013 Dihedral : 8.042 109.324 1713 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 1.69 % Allowed : 15.63 % Favored : 82.68 % 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: 0.92 (0.23), residues: 1401 helix: 1.17 (0.21), residues: 626 sheet: 0.97 (0.35), residues: 194 loop : -0.02 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE A 955 TYR 0.018 0.001 TYR A 476 ARG 0.019 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.06 seconds wall clock time: 69 minutes 43.08 seconds (4183.08 seconds total)