Starting phenix.real_space_refine on Fri Mar 15 08:54:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxa_17262/03_2024/8oxa_17262_updated.pdb" } resolution = 2.76 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7196 2.51 5 N 1833 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "A TYR 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "B PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'D39': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 6.35, per 1000 atoms: 0.57 Number of scatterers: 11138 At special positions: 0 Unit cell: (90.4183, 90.4183, 178.734, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2052 8.00 N 1833 7.00 C 7196 6.00 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: 4.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 10 sheets defined 44.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.009A pdb=" N GLN A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 116 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 142 through 174 removed outlier: 3.677A pdb=" N VAL A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.780A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (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 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' Processing helix chain 'A' and resid 253 through 257 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 318 through 321 No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 332 through 365 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.600A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 402 through 420 removed outlier: 3.594A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 removed outlier: 3.521A pdb=" N GLY A 446 " --> pdb=" O GLU A 443 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 553 through 564 Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.642A pdb=" N ARG A 628 " --> pdb=" O VAL A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'A' and resid 684 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 769 removed outlier: 3.562A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 794 No H-bonds generated for 'chain 'A' and resid 792 through 794' Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 840 through 859 removed outlier: 3.623A pdb=" N GLU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 884 removed outlier: 3.515A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 4.658A pdb=" N ASN A 899 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.690A pdb=" N LEU A 935 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 937 " --> pdb=" O ARG A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 962 removed outlier: 3.562A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 removed outlier: 4.286A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 971 " --> pdb=" O TRP A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 3.619A pdb=" N LEU A 987 " --> pdb=" O TRP A 983 " (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 1056 Proline residue: A1051 - end of helix Processing helix chain 'A' and resid 1069 through 1091 removed outlier: 3.501A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1113 removed outlier: 3.564A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1141 removed outlier: 4.142A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1141' 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 73 Proline residue: B 52 - end of helix removed outlier: 3.943A 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 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' 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 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' 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 removed outlier: 3.663A pdb=" N PHE B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 Processing sheet with id= B, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= C, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.784A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 224 through 226 Processing sheet with id= E, first strand: chain 'A' and resid 277 through 281 removed outlier: 3.862A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 906 through 909 removed outlier: 6.446A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS A 727 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER A 453 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP A 729 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 863 " --> pdb=" O VAL A 730 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 584 through 588 removed outlier: 6.754A pdb=" N SER A 580 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE A 569 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 464 through 471 removed outlier: 6.811A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 703 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 654 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 705 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG A 652 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.511A pdb=" N ARG B 307 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.314A 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 110 removed outlier: 4.073A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1221 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: 3.95 Time building geometry restraints manager: 4.85 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: 1785 1.31 - 1.44: 3165 1.44 - 1.56: 6344 1.56 - 1.69: 6 1.69 - 1.82: 83 Bond restraints: 11383 Sorted by residual: bond pdb=" C15 D39 A1203 " pdb=" C16 D39 A1203 " ideal model delta sigma weight residual 1.594 1.523 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C28 D39 A1203 " pdb=" C29 D39 A1203 " ideal model delta sigma weight residual 1.603 1.535 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C13 D39 A1203 " pdb=" C14 D39 A1203 " ideal model delta sigma weight residual 1.581 1.516 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C12 D39 A1203 " pdb=" C13 D39 A1203 " ideal model delta sigma weight residual 1.573 1.521 0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C5 D39 A1203 " pdb=" O4 D39 A1203 " ideal model delta sigma weight residual 1.453 1.402 0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 11378 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.65: 142 104.65 - 111.97: 5526 111.97 - 119.30: 3831 119.30 - 126.63: 5757 126.63 - 133.96: 160 Bond angle restraints: 15416 Sorted by residual: angle pdb=" N PRO B 87 " pdb=" CD PRO B 87 " pdb=" CG PRO B 87 " ideal model delta sigma weight residual 103.20 97.78 5.42 1.50e+00 4.44e-01 1.31e+01 angle pdb=" CA PRO B 87 " pdb=" N PRO B 87 " pdb=" CD PRO B 87 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.30 6.00 2.00e+00 2.50e-01 9.01e+00 angle pdb=" N ALA A1065 " pdb=" CA ALA A1065 " pdb=" C ALA A1065 " ideal model delta sigma weight residual 108.82 113.75 -4.93 1.69e+00 3.50e-01 8.50e+00 angle pdb=" C PRO A1066 " pdb=" N SER A1067 " pdb=" CA SER A1067 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 ... (remaining 15411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 6516 27.54 - 55.07: 263 55.07 - 82.61: 30 82.61 - 110.15: 13 110.15 - 137.68: 1 Dihedral angle restraints: 6823 sinusoidal: 2831 harmonic: 3992 Sorted by residual: dihedral pdb=" C31 D39 A1203 " pdb=" C32 D39 A1203 " pdb=" C33 D39 A1203 " pdb=" C34 D39 A1203 " ideal model delta sinusoidal sigma weight residual 135.11 -87.21 -137.68 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.66 108.37 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.71 106.33 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 6820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1478 0.054 - 0.107: 205 0.107 - 0.161: 42 0.161 - 0.215: 1 0.215 - 0.269: 1 Chirality restraints: 1727 Sorted by residual: 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 1.80e+00 chirality pdb=" CB THR A1152 " pdb=" CA THR A1152 " pdb=" OG1 THR A1152 " pdb=" CG2 THR A1152 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1724 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 793 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 109 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 195 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 196 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.022 5.00e-02 4.00e+02 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 8443 3.11 - 3.70: 17126 3.70 - 4.30: 26303 4.30 - 4.90: 43244 Nonbonded interactions: 95191 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 1.910 3.040 nonbonded pdb=" O GLN A 65 " pdb=" OH TYR A 92 " model vdw 1.995 2.440 nonbonded pdb=" OG1 THR A 732 " pdb=" O1 VN4 A1201 " model vdw 2.018 2.440 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 2.031 2.170 nonbonded pdb=" O THR A 456 " pdb="MG MG A1202 " model vdw 2.052 2.170 ... (remaining 95186 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: 1.140 Set stop_for_unknowns flag: 0.010 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: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.380 Find NCS groups from input model: 0.300 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 0.071 11383 Z= 0.216 Angle : 0.534 8.785 15416 Z= 0.273 Chirality : 0.040 0.269 1727 Planarity : 0.004 0.061 1939 Dihedral : 15.253 137.682 4242 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -0.27 (0.23), residues: 1349 helix: 0.45 (0.22), residues: 609 sheet: 0.12 (0.38), residues: 203 loop : -0.91 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.002 0.000 HIS A 479 PHE 0.012 0.001 PHE A 466 TYR 0.009 0.001 TYR A 225 ARG 0.003 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8110 (ttpt) REVERT: A 526 GLN cc_start: 0.7872 (mm110) cc_final: 0.7136 (mm110) REVERT: A 640 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7642 (mm-40) REVERT: A 644 ASP cc_start: 0.7853 (m-30) cc_final: 0.7388 (m-30) REVERT: B 195 ILE cc_start: 0.7783 (mt) cc_final: 0.7447 (tt) REVERT: B 337 PHE cc_start: 0.7219 (m-80) cc_final: 0.7009 (m-80) outliers start: 0 outliers final: 1 residues processed: 152 average time/residue: 1.0592 time to fit residues: 176.6870 Evaluate side-chains 117 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 0.0060 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11383 Z= 0.265 Angle : 0.574 9.040 15416 Z= 0.295 Chirality : 0.042 0.237 1727 Planarity : 0.004 0.055 1939 Dihedral : 9.449 93.798 1626 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.09 % Allowed : 7.10 % Favored : 90.81 % 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: 0.12 (0.23), residues: 1349 helix: 0.91 (0.21), residues: 616 sheet: 0.19 (0.37), residues: 214 loop : -0.91 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.003 0.001 HIS A 359 PHE 0.014 0.002 PHE A 666 TYR 0.013 0.001 TYR A1144 ARG 0.006 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.216 Fit side-chains REVERT: A 526 GLN cc_start: 0.7802 (mm110) cc_final: 0.7578 (mm-40) REVERT: A 640 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7713 (mm-40) REVERT: A 644 ASP cc_start: 0.7706 (m-30) cc_final: 0.7199 (m-30) REVERT: B 166 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (ptmt) REVERT: B 195 ILE cc_start: 0.7764 (mt) cc_final: 0.7443 (tt) REVERT: B 200 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7653 (ptpp) outliers start: 25 outliers final: 15 residues processed: 133 average time/residue: 0.9926 time to fit residues: 145.7588 Evaluate side-chains 121 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 237 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 447 GLN A 597 ASN A1138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11383 Z= 0.264 Angle : 0.552 9.528 15416 Z= 0.280 Chirality : 0.042 0.247 1727 Planarity : 0.004 0.054 1939 Dihedral : 8.292 89.514 1624 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.92 % Allowed : 10.36 % Favored : 86.72 % 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: 0.13 (0.23), residues: 1349 helix: 0.99 (0.21), residues: 618 sheet: 0.22 (0.38), residues: 215 loop : -1.03 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 669 HIS 0.002 0.001 HIS A 479 PHE 0.016 0.002 PHE A 239 TYR 0.016 0.001 TYR A1144 ARG 0.005 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 1.353 Fit side-chains REVERT: A 526 GLN cc_start: 0.7788 (mm110) cc_final: 0.7054 (mm110) REVERT: A 640 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7743 (mm-40) REVERT: A 644 ASP cc_start: 0.7578 (m-30) cc_final: 0.6990 (m-30) REVERT: B 200 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7616 (ptpp) REVERT: B 261 MET cc_start: 0.8336 (mmm) cc_final: 0.8093 (mmm) REVERT: B 337 PHE cc_start: 0.7129 (m-80) cc_final: 0.6760 (t80) outliers start: 35 outliers final: 19 residues processed: 132 average time/residue: 1.0383 time to fit residues: 151.3083 Evaluate side-chains 124 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 447 GLN A 526 GLN A 597 ASN A 917 GLN A1179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11383 Z= 0.255 Angle : 0.551 11.974 15416 Z= 0.280 Chirality : 0.042 0.248 1727 Planarity : 0.004 0.053 1939 Dihedral : 7.632 89.253 1624 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.51 % Allowed : 11.70 % Favored : 84.80 % 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: 0.12 (0.23), residues: 1349 helix: 1.00 (0.21), residues: 621 sheet: 0.25 (0.37), residues: 217 loop : -1.10 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 669 HIS 0.002 0.001 HIS A 939 PHE 0.019 0.002 PHE A 666 TYR 0.014 0.001 TYR A1144 ARG 0.004 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.234 Fit side-chains REVERT: A 526 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7039 (mm110) REVERT: A 627 GLU cc_start: 0.8146 (tt0) cc_final: 0.7936 (pt0) REVERT: A 640 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7744 (mm-40) REVERT: A 644 ASP cc_start: 0.7564 (m-30) cc_final: 0.7046 (m-30) REVERT: B 42 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: B 200 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7611 (ptpp) REVERT: B 337 PHE cc_start: 0.7217 (m-80) cc_final: 0.6885 (t80) outliers start: 42 outliers final: 22 residues processed: 136 average time/residue: 1.0021 time to fit residues: 150.0465 Evaluate side-chains 124 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN A 547 ASN A 597 ASN A 633 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11383 Z= 0.206 Angle : 0.524 10.549 15416 Z= 0.267 Chirality : 0.041 0.251 1727 Planarity : 0.004 0.052 1939 Dihedral : 7.148 89.505 1624 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.26 % Allowed : 13.20 % Favored : 83.54 % 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: 0.23 (0.23), residues: 1349 helix: 1.09 (0.21), residues: 621 sheet: 0.28 (0.37), residues: 213 loop : -1.03 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.002 0.001 HIS A 939 PHE 0.024 0.001 PHE A 666 TYR 0.011 0.001 TYR A1144 ARG 0.004 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 1.012 Fit side-chains REVERT: A 271 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7296 (mpp-170) REVERT: A 526 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7034 (mm110) REVERT: A 640 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7745 (mm-40) REVERT: A 644 ASP cc_start: 0.7569 (m-30) cc_final: 0.7064 (m-30) REVERT: A 700 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7902 (tp) REVERT: B 42 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8332 (mm-40) REVERT: B 200 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7590 (ptpp) REVERT: B 337 PHE cc_start: 0.7229 (m-80) cc_final: 0.6899 (t80) outliers start: 39 outliers final: 21 residues processed: 131 average time/residue: 1.0011 time to fit residues: 144.6816 Evaluate side-chains 126 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 130 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 447 GLN A 547 ASN A 597 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11383 Z= 0.191 Angle : 0.517 9.596 15416 Z= 0.263 Chirality : 0.040 0.252 1727 Planarity : 0.004 0.050 1939 Dihedral : 6.842 87.971 1624 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.01 % Allowed : 14.37 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1349 helix: 1.19 (0.22), residues: 621 sheet: 0.31 (0.37), residues: 213 loop : -1.00 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 PHE 0.027 0.001 PHE A 666 TYR 0.012 0.001 TYR A1144 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.393 Fit side-chains REVERT: A 526 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7074 (mm110) REVERT: A 640 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7732 (mm-40) REVERT: A 644 ASP cc_start: 0.7560 (m-30) cc_final: 0.7042 (m-30) REVERT: A 700 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8007 (tp) REVERT: B 42 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8281 (mm-40) REVERT: B 200 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7593 (ptpp) REVERT: B 337 PHE cc_start: 0.7253 (m-80) cc_final: 0.6931 (t80) outliers start: 36 outliers final: 21 residues processed: 131 average time/residue: 0.9934 time to fit residues: 143.7243 Evaluate side-chains 128 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.0370 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 442 ASN A 447 GLN A 474 GLN A 547 ASN A 597 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11383 Z= 0.291 Angle : 0.556 9.611 15416 Z= 0.283 Chirality : 0.042 0.250 1727 Planarity : 0.004 0.049 1939 Dihedral : 6.784 84.970 1624 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.43 % Allowed : 14.54 % Favored : 82.04 % 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: 0.20 (0.23), residues: 1349 helix: 1.12 (0.22), residues: 610 sheet: 0.25 (0.37), residues: 207 loop : -1.04 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 669 HIS 0.003 0.001 HIS A 417 PHE 0.028 0.002 PHE A 666 TYR 0.015 0.002 TYR A1144 ARG 0.005 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 1.279 Fit side-chains REVERT: A 271 ARG cc_start: 0.7791 (mpp-170) cc_final: 0.7220 (mpp-170) REVERT: A 365 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7031 (mt0) REVERT: A 526 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7115 (mm110) REVERT: A 640 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7705 (mm-40) REVERT: A 644 ASP cc_start: 0.7528 (m-30) cc_final: 0.7031 (m-30) REVERT: A 700 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 42 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8370 (mm-40) REVERT: B 200 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7599 (ptpp) REVERT: B 337 PHE cc_start: 0.7284 (m-80) cc_final: 0.6994 (t80) outliers start: 41 outliers final: 25 residues processed: 133 average time/residue: 1.0270 time to fit residues: 150.5604 Evaluate side-chains 135 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN A 547 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11383 Z= 0.188 Angle : 0.522 9.598 15416 Z= 0.266 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.049 1939 Dihedral : 6.569 83.965 1624 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.92 % Allowed : 15.46 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1349 helix: 1.13 (0.22), residues: 623 sheet: 0.33 (0.37), residues: 213 loop : -0.90 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.002 0.001 HIS A 939 PHE 0.029 0.001 PHE A 666 TYR 0.014 0.001 TYR A1144 ARG 0.006 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.272 Fit side-chains REVERT: A 526 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7080 (mm110) REVERT: A 640 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7722 (mm-40) REVERT: A 644 ASP cc_start: 0.7535 (m-30) cc_final: 0.7047 (m-30) REVERT: A 700 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8078 (tp) REVERT: B 42 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (mm-40) REVERT: B 166 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7658 (ptmt) REVERT: B 200 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7609 (ptpp) REVERT: B 337 PHE cc_start: 0.7254 (m-80) cc_final: 0.6976 (t80) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 1.0144 time to fit residues: 146.1533 Evaluate side-chains 133 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 124 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11383 Z= 0.229 Angle : 0.534 9.605 15416 Z= 0.272 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.048 1939 Dihedral : 6.436 80.977 1624 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.92 % Allowed : 15.62 % Favored : 81.45 % 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: 0.27 (0.23), residues: 1349 helix: 1.02 (0.21), residues: 632 sheet: 0.45 (0.37), residues: 202 loop : -0.94 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 PHE 0.027 0.002 PHE A 666 TYR 0.014 0.001 TYR A1144 ARG 0.003 0.000 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.313 Fit side-chains REVERT: A 271 ARG cc_start: 0.7708 (mpp-170) cc_final: 0.7182 (mpp-170) REVERT: A 365 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7020 (mt0) REVERT: A 526 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7058 (mm110) REVERT: A 640 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7718 (mm-40) REVERT: A 644 ASP cc_start: 0.7489 (m-30) cc_final: 0.6998 (m-30) REVERT: A 700 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8126 (tp) REVERT: B 42 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: B 166 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: B 200 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7612 (ptpp) REVERT: B 337 PHE cc_start: 0.7260 (m-80) cc_final: 0.6990 (t80) outliers start: 35 outliers final: 27 residues processed: 128 average time/residue: 1.0598 time to fit residues: 149.3556 Evaluate side-chains 137 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 398 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 590 VAL Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11383 Z= 0.211 Angle : 0.532 9.599 15416 Z= 0.271 Chirality : 0.041 0.250 1727 Planarity : 0.004 0.049 1939 Dihedral : 6.354 79.606 1624 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.59 % Allowed : 16.21 % Favored : 81.20 % 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: 0.29 (0.23), residues: 1349 helix: 1.04 (0.21), residues: 632 sheet: 0.46 (0.37), residues: 204 loop : -0.93 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 669 HIS 0.002 0.001 HIS A 417 PHE 0.025 0.001 PHE A 666 TYR 0.017 0.001 TYR A1144 ARG 0.003 0.000 ARG A 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 1.342 Fit side-chains REVERT: A 271 ARG cc_start: 0.7689 (mpp-170) cc_final: 0.7169 (mpp-170) REVERT: A 365 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: A 526 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7047 (mm110) REVERT: A 640 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7715 (mm-40) REVERT: A 644 ASP cc_start: 0.7481 (m-30) cc_final: 0.6980 (m-30) REVERT: A 700 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 42 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: B 166 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (ptmt) REVERT: B 200 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7613 (ptpp) REVERT: B 337 PHE cc_start: 0.7252 (m-80) cc_final: 0.6986 (t80) outliers start: 31 outliers final: 24 residues processed: 125 average time/residue: 1.0691 time to fit residues: 146.9804 Evaluate side-chains 133 residues out of total 1197 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 107 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 94 optimal weight: 0.5980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A1099 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117156 restraints weight = 12013.050| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.01 r_work: 0.3289 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11383 Z= 0.140 Angle : 0.497 9.589 15416 Z= 0.255 Chirality : 0.040 0.249 1727 Planarity : 0.004 0.048 1939 Dihedral : 5.988 76.641 1624 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.26 % Allowed : 16.54 % Favored : 81.20 % 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 (0.24), residues: 1349 helix: 1.27 (0.22), residues: 635 sheet: 0.45 (0.37), residues: 215 loop : -0.88 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 669 HIS 0.002 0.000 HIS A 449 PHE 0.023 0.001 PHE A 239 TYR 0.011 0.001 TYR B 121 ARG 0.004 0.000 ARG B 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.39 seconds wall clock time: 64 minutes 33.00 seconds (3873.00 seconds total)