Starting phenix.real_space_refine on Sat Feb 17 13:04:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7voo_32052/02_2024/7voo_32052_updated.pdb" } resolution = 3.9 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= 0.007 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9113 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6140 2.51 5 N 1609 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 941": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9521 Classifications: {'peptide': 1245} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 61, 'TRANS': 1183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'MEQ:plan-2': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 107 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.51, per 1000 atoms: 0.57 Number of scatterers: 9686 At special positions: 0 Unit cell: (99.84, 125.84, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1894 8.00 N 1609 7.00 C 6140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2101 " - " ASN A 70 " " NAG A2102 " - " ASN A 247 " " NAG A2103 " - " ASN A 396 " " NAG B 1 " - " ASN A 55 " " NAG C 1 " - " ASN A 410 " " NAG D 1 " - " ASN A 869 " " NAG E 1 " - " ASN A 991 " Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 19 sheets defined 16.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 617 through 621 removed outlier: 3.869A pdb=" N LEU A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 621' Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 973 through 992 removed outlier: 3.685A pdb=" N ASN A 976 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 980 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) Proline residue: A 982 - end of helix removed outlier: 3.835A pdb=" N VAL A 986 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 removed outlier: 3.589A pdb=" N GLY A1006 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1040 through 1054 removed outlier: 4.887A pdb=" N ALA A1054 " --> pdb=" O ALA A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1070 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 removed outlier: 3.606A pdb=" N PHE A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A1127 " --> pdb=" O ASN A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 Processing helix chain 'A' and resid 1160 through 1172 removed outlier: 4.397A pdb=" N GLU A1165 " --> pdb=" O ASP A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 3.802A pdb=" N THR A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1240 removed outlier: 4.054A pdb=" N ASN A1233 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A1234 " --> pdb=" O SER A1230 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP A1237 " --> pdb=" O ASN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1246 No H-bonds generated for 'chain 'A' and resid 1244 through 1246' Processing helix chain 'A' and resid 1252 through 1268 Processing helix chain 'A' and resid 1294 through 1296 No H-bonds generated for 'chain 'A' and resid 1294 through 1296' Processing sheet with id= A, first strand: chain 'A' and resid 675 through 679 removed outlier: 3.800A pdb=" N VAL A 35 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LYS A 46 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 49 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A 85 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.925A pdb=" N VAL A 60 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 147 through 149 Processing sheet with id= D, first strand: chain 'A' and resid 214 through 219 removed outlier: 4.012A pdb=" N LEU A 164 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA A 176 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.504A pdb=" N GLN A 232 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 251 " --> pdb=" O GLN A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 287 through 292 removed outlier: 3.514A pdb=" N VAL A 264 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 321 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 404 through 409 removed outlier: 3.865A pdb=" N VAL A 369 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 407 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 365 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG A 370 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 352 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL A 372 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 350 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 396 through 398 Processing sheet with id= I, first strand: chain 'A' and resid 458 through 461 removed outlier: 3.732A pdb=" N PHE A 458 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 474 through 476 Processing sheet with id= K, first strand: chain 'A' and resid 552 through 559 removed outlier: 3.909A pdb=" N ILE A 552 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 541 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 543 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 496 " --> pdb=" O TYR A 543 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 497 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA A 501 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 569 through 571 Processing sheet with id= M, first strand: chain 'A' and resid 742 through 745 Processing sheet with id= N, first strand: chain 'A' and resid 792 through 797 removed outlier: 3.626A pdb=" N GLY A 852 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.760A pdb=" N LEU A 904 " --> pdb=" O VAL A 802 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'A' and resid 846 through 848 removed outlier: 4.471A pdb=" N HIS A 846 " --> pdb=" O VAL A 824 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 824 " --> pdb=" O HIS A 846 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 848 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 822 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 872 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 910 through 915 Processing sheet with id= R, first strand: chain 'A' and resid 918 through 920 Processing sheet with id= S, first strand: chain 'A' and resid 925 through 931 removed outlier: 3.634A pdb=" N GLY A 925 " --> pdb=" O GLY A1318 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A1312 " --> pdb=" O LEU A 931 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 771 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: 3.39 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3135 1.34 - 1.46: 2226 1.46 - 1.58: 4463 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 9887 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" CA GLN A 232 " pdb=" CB GLN A 232 " ideal model delta sigma weight residual 1.524 1.568 -0.044 1.62e-02 3.81e+03 7.45e+00 bond pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.05e-02 9.07e+03 4.03e+00 bond pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.58e-02 4.01e+03 2.96e+00 ... (remaining 9882 not shown) Histogram of bond angle deviations from ideal: 94.94 - 104.18: 164 104.18 - 113.42: 5709 113.42 - 122.66: 6211 122.66 - 131.90: 1352 131.90 - 141.14: 11 Bond angle restraints: 13447 Sorted by residual: angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CA PRO A 657 " ideal model delta sigma weight residual 119.84 141.14 -21.30 1.25e+00 6.40e-01 2.90e+02 angle pdb=" N PHE A 309 " pdb=" CA PHE A 309 " pdb=" C PHE A 309 " ideal model delta sigma weight residual 109.62 94.94 14.68 1.50e+00 4.44e-01 9.58e+01 angle pdb=" C THR A 656 " pdb=" N PRO A 657 " pdb=" CD PRO A 657 " ideal model delta sigma weight residual 125.00 99.79 25.21 4.10e+00 5.95e-02 3.78e+01 angle pdb=" N GLY A 652 " pdb=" CA GLY A 652 " pdb=" C GLY A 652 " ideal model delta sigma weight residual 113.18 98.93 14.25 2.37e+00 1.78e-01 3.61e+01 angle pdb=" CA PRO A 261 " pdb=" C PRO A 261 " pdb=" N GLY A 262 " ideal model delta sigma weight residual 115.78 109.68 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 13442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5734 24.18 - 48.37: 261 48.37 - 72.55: 22 72.55 - 96.73: 34 96.73 - 120.92: 54 Dihedral angle restraints: 6105 sinusoidal: 2488 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS A 821 " pdb=" SG CYS A 821 " pdb=" SG CYS A 849 " pdb=" CB CYS A 849 " ideal model delta sinusoidal sigma weight residual -86.00 -134.01 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA ARG A 684 " pdb=" C ARG A 684 " pdb=" N LYS A 685 " pdb=" CA LYS A 685 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C THR A 656 " pdb=" N THR A 656 " pdb=" CA THR A 656 " pdb=" CB THR A 656 " ideal model delta harmonic sigma weight residual -122.00 -133.87 11.87 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 6102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1509 0.098 - 0.196: 72 0.196 - 0.294: 5 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 1590 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 410 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 55 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA THR A 656 " pdb=" N THR A 656 " pdb=" C THR A 656 " pdb=" CB THR A 656 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 1587 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 656 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 657 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 308 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C VAL A 308 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL A 308 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 309 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 578 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO A 579 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.027 5.00e-02 4.00e+02 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 97 2.52 - 3.12: 7701 3.12 - 3.71: 15164 3.71 - 4.31: 20443 4.31 - 4.90: 33055 Nonbonded interactions: 76460 Sorted by model distance: nonbonded pdb=" O ASP A 665 " pdb=" OG SER A 668 " model vdw 1.930 2.440 nonbonded pdb=" O GLN A 132 " pdb=" OG1 THR A 133 " model vdw 2.063 2.440 nonbonded pdb=" NH2 ARG A 823 " pdb=" O GLN A 880 " model vdw 2.099 2.520 nonbonded pdb=" O MET A 318 " pdb=" OG SER A 341 " model vdw 2.161 2.440 nonbonded pdb=" O CYS A1079 " pdb=" OG SER A1102 " model vdw 2.172 2.440 ... (remaining 76455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 5.660 Check model and map are aligned: 0.000 Set scattering table: 0.090 Process input model: 29.480 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 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 0.077 9887 Z= 0.277 Angle : 0.912 25.209 13447 Z= 0.498 Chirality : 0.052 0.490 1590 Planarity : 0.005 0.114 1717 Dihedral : 19.361 120.917 3749 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.72 % Favored : 86.87 % Rotamer: Outliers : 0.29 % Allowed : 0.67 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.23), residues: 1234 helix: 0.10 (0.38), residues: 195 sheet: -1.48 (0.26), residues: 405 loop : -3.06 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1069 HIS 0.003 0.001 HIS A1259 PHE 0.030 0.002 PHE A1057 TYR 0.026 0.002 TYR A 667 ARG 0.007 0.001 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 500 MET cc_start: 0.8231 (mtp) cc_final: 0.7901 (mtp) REVERT: A 673 MET cc_start: 0.8988 (tpp) cc_final: 0.8661 (tpp) REVERT: A 1323 TYR cc_start: 0.7028 (t80) cc_final: 0.6591 (t80) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.1956 time to fit residues: 37.5544 Evaluate side-chains 99 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 40.0000 chunk 112 optimal weight: 10.0000 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9887 Z= 0.240 Angle : 0.783 10.795 13447 Z= 0.386 Chirality : 0.051 0.382 1590 Planarity : 0.005 0.133 1717 Dihedral : 19.689 109.243 1572 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.32 % Favored : 87.36 % Rotamer: Outliers : 2.02 % Allowed : 8.85 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 1234 helix: 0.17 (0.38), residues: 195 sheet: -1.42 (0.26), residues: 425 loop : -3.03 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 739 HIS 0.018 0.001 HIS A 358 PHE 0.013 0.002 PHE A 74 TYR 0.024 0.002 TYR A 496 ARG 0.005 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6340 (ptp) cc_final: 0.6025 (ptm) REVERT: A 554 ASP cc_start: 0.6278 (t0) cc_final: 0.5951 (m-30) REVERT: A 989 TYR cc_start: 0.7989 (t80) cc_final: 0.7661 (t80) REVERT: A 1323 TYR cc_start: 0.6855 (t80) cc_final: 0.6344 (t80) outliers start: 21 outliers final: 13 residues processed: 116 average time/residue: 0.2113 time to fit residues: 36.3112 Evaluate side-chains 110 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 100 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9887 Z= 0.241 Angle : 0.751 10.242 13447 Z= 0.366 Chirality : 0.050 0.395 1590 Planarity : 0.005 0.122 1717 Dihedral : 17.483 106.723 1572 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.07 % Favored : 87.60 % Rotamer: Outliers : 2.50 % Allowed : 12.98 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1234 helix: 0.30 (0.38), residues: 199 sheet: -1.32 (0.25), residues: 425 loop : -2.95 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 739 HIS 0.014 0.001 HIS A 358 PHE 0.014 0.002 PHE A 385 TYR 0.018 0.001 TYR A 667 ARG 0.006 0.001 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.6523 (ptp) cc_final: 0.6251 (ptm) REVERT: A 554 ASP cc_start: 0.6339 (t0) cc_final: 0.5981 (m-30) REVERT: A 673 MET cc_start: 0.8838 (tpp) cc_final: 0.8483 (mmm) outliers start: 26 outliers final: 15 residues processed: 111 average time/residue: 0.1767 time to fit residues: 30.5294 Evaluate side-chains 105 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9887 Z= 0.259 Angle : 0.757 10.018 13447 Z= 0.367 Chirality : 0.050 0.413 1590 Planarity : 0.005 0.118 1717 Dihedral : 16.181 105.574 1572 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.07 % Favored : 87.60 % Rotamer: Outliers : 3.65 % Allowed : 14.71 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.24), residues: 1234 helix: 0.33 (0.38), residues: 199 sheet: -1.30 (0.25), residues: 431 loop : -2.90 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 739 HIS 0.011 0.001 HIS A 358 PHE 0.015 0.002 PHE A 524 TYR 0.017 0.002 TYR A1145 ARG 0.003 0.001 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8478 (m-40) cc_final: 0.8236 (p0) REVERT: A 203 TYR cc_start: 0.6248 (m-10) cc_final: 0.5996 (m-10) REVERT: A 554 ASP cc_start: 0.6376 (t0) cc_final: 0.5939 (m-30) REVERT: A 989 TYR cc_start: 0.7711 (t80) cc_final: 0.7282 (t80) REVERT: A 1214 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8605 (mm) outliers start: 38 outliers final: 26 residues processed: 116 average time/residue: 0.1680 time to fit residues: 30.0784 Evaluate side-chains 117 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 963 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9887 Z= 0.273 Angle : 0.766 10.027 13447 Z= 0.371 Chirality : 0.050 0.417 1590 Planarity : 0.005 0.116 1717 Dihedral : 15.221 104.126 1572 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.56 % Favored : 87.12 % Rotamer: Outliers : 4.52 % Allowed : 15.48 % Favored : 80.00 % 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: -2.69 (0.24), residues: 1234 helix: 0.30 (0.38), residues: 205 sheet: -1.37 (0.25), residues: 437 loop : -2.92 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 739 HIS 0.009 0.001 HIS A 358 PHE 0.025 0.002 PHE A 130 TYR 0.024 0.002 TYR A 619 ARG 0.003 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 87 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 132 GLN cc_start: 0.4656 (OUTLIER) cc_final: 0.3720 (mt0) REVERT: A 238 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (pt) REVERT: A 318 MET cc_start: 0.6505 (mtt) cc_final: 0.6235 (mpp) REVERT: A 554 ASP cc_start: 0.6363 (t0) cc_final: 0.5965 (m-30) REVERT: A 989 TYR cc_start: 0.7761 (t80) cc_final: 0.7404 (t80) REVERT: A 1214 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8618 (mm) outliers start: 47 outliers final: 29 residues processed: 116 average time/residue: 0.1704 time to fit residues: 30.5064 Evaluate side-chains 120 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9887 Z= 0.423 Angle : 0.869 10.166 13447 Z= 0.433 Chirality : 0.054 0.435 1590 Planarity : 0.006 0.119 1717 Dihedral : 15.165 104.771 1572 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.59 % Favored : 85.09 % Rotamer: Outliers : 5.10 % Allowed : 16.44 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.23), residues: 1234 helix: 0.08 (0.38), residues: 197 sheet: -1.68 (0.25), residues: 450 loop : -2.84 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 739 HIS 0.010 0.002 HIS A1062 PHE 0.028 0.002 PHE A 130 TYR 0.030 0.002 TYR A 985 ARG 0.005 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 92 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.5213 (OUTLIER) cc_final: 0.3977 (mt0) REVERT: A 154 ASN cc_start: 0.8595 (m-40) cc_final: 0.8261 (p0) REVERT: A 238 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (pt) REVERT: A 554 ASP cc_start: 0.6362 (t0) cc_final: 0.6022 (m-30) REVERT: A 673 MET cc_start: 0.8765 (tpp) cc_final: 0.8296 (tmm) REVERT: A 989 TYR cc_start: 0.7971 (t80) cc_final: 0.7623 (t80) REVERT: A 1062 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.6154 (t-90) outliers start: 53 outliers final: 35 residues processed: 130 average time/residue: 0.1890 time to fit residues: 36.9399 Evaluate side-chains 126 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1062 HIS Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.3980 chunk 13 optimal weight: 0.0000 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9887 Z= 0.209 Angle : 0.758 10.933 13447 Z= 0.363 Chirality : 0.050 0.421 1590 Planarity : 0.005 0.116 1717 Dihedral : 14.255 102.886 1572 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.26 % Favored : 88.41 % Rotamer: Outliers : 3.85 % Allowed : 18.75 % Favored : 77.40 % 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: -2.60 (0.24), residues: 1234 helix: 0.34 (0.38), residues: 196 sheet: -1.32 (0.25), residues: 437 loop : -2.80 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1069 HIS 0.008 0.001 HIS A 358 PHE 0.026 0.002 PHE A 130 TYR 0.021 0.002 TYR A 667 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 96 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.5290 (m-80) REVERT: A 154 ASN cc_start: 0.8302 (m-40) cc_final: 0.7974 (p0) REVERT: A 238 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (pt) REVERT: A 464 MET cc_start: 0.8312 (mtt) cc_final: 0.7973 (mtp) REVERT: A 495 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: A 554 ASP cc_start: 0.5833 (t0) cc_final: 0.5482 (m-30) REVERT: A 988 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8247 (t70) REVERT: A 989 TYR cc_start: 0.7493 (t80) cc_final: 0.7252 (t80) outliers start: 40 outliers final: 30 residues processed: 120 average time/residue: 0.1819 time to fit residues: 32.9757 Evaluate side-chains 121 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9887 Z= 0.429 Angle : 0.876 10.530 13447 Z= 0.434 Chirality : 0.053 0.436 1590 Planarity : 0.006 0.119 1717 Dihedral : 14.598 103.211 1572 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 27.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.15 % Favored : 84.52 % Rotamer: Outliers : 4.62 % Allowed : 18.94 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.24), residues: 1234 helix: -0.05 (0.38), residues: 198 sheet: -1.60 (0.25), residues: 446 loop : -2.79 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 739 HIS 0.010 0.002 HIS A1062 PHE 0.032 0.002 PHE A 130 TYR 0.029 0.003 TYR A 985 ARG 0.007 0.001 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 92 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8530 (m-40) cc_final: 0.8144 (p0) REVERT: A 238 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8206 (pt) REVERT: A 464 MET cc_start: 0.8400 (mtt) cc_final: 0.8003 (mtp) REVERT: A 495 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: A 554 ASP cc_start: 0.6510 (t0) cc_final: 0.6155 (m-30) REVERT: A 848 ILE cc_start: 0.2125 (OUTLIER) cc_final: 0.0979 (pt) REVERT: A 988 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8429 (t70) REVERT: A 989 TYR cc_start: 0.7875 (t80) cc_final: 0.7574 (t80) REVERT: A 1062 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6213 (t-90) REVERT: A 1070 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6816 (mp) outliers start: 48 outliers final: 34 residues processed: 126 average time/residue: 0.1856 time to fit residues: 35.9611 Evaluate side-chains 130 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1062 HIS Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9887 Z= 0.224 Angle : 0.781 10.124 13447 Z= 0.374 Chirality : 0.051 0.424 1590 Planarity : 0.005 0.118 1717 Dihedral : 13.819 100.799 1572 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.35 % Favored : 88.33 % Rotamer: Outliers : 3.94 % Allowed : 20.00 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.24), residues: 1234 helix: 0.34 (0.38), residues: 196 sheet: -1.32 (0.25), residues: 435 loop : -2.77 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1237 HIS 0.005 0.001 HIS A 460 PHE 0.032 0.002 PHE A 130 TYR 0.025 0.002 TYR A 970 ARG 0.007 0.001 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 93 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8279 (m-40) cc_final: 0.7975 (p0) REVERT: A 238 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8185 (pt) REVERT: A 464 MET cc_start: 0.8352 (mtt) cc_final: 0.7966 (mtp) REVERT: A 495 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 554 ASP cc_start: 0.6179 (t0) cc_final: 0.5839 (m-30) REVERT: A 673 MET cc_start: 0.9067 (tpp) cc_final: 0.8706 (tpp) REVERT: A 988 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8255 (t70) REVERT: A 989 TYR cc_start: 0.7455 (t80) cc_final: 0.7224 (t80) outliers start: 41 outliers final: 29 residues processed: 120 average time/residue: 0.1762 time to fit residues: 32.4338 Evaluate side-chains 122 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 81 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 40.0000 chunk 60 optimal weight: 0.0020 chunk 78 optimal weight: 10.0000 overall best weight: 3.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9887 Z= 0.290 Angle : 0.797 10.535 13447 Z= 0.385 Chirality : 0.051 0.434 1590 Planarity : 0.005 0.118 1717 Dihedral : 13.683 98.058 1572 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.86 % Favored : 85.82 % Rotamer: Outliers : 3.46 % Allowed : 20.67 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1234 helix: 0.34 (0.38), residues: 197 sheet: -1.36 (0.25), residues: 436 loop : -2.75 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 739 HIS 0.009 0.001 HIS A1062 PHE 0.029 0.002 PHE A 130 TYR 0.026 0.002 TYR A 970 ARG 0.007 0.001 ARG A 787 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.4908 (OUTLIER) cc_final: 0.3932 (mt0) REVERT: A 154 ASN cc_start: 0.8356 (m-40) cc_final: 0.8060 (p0) REVERT: A 238 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8197 (pt) REVERT: A 464 MET cc_start: 0.8410 (mtt) cc_final: 0.8000 (mtp) REVERT: A 495 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: A 554 ASP cc_start: 0.6468 (t0) cc_final: 0.6066 (m-30) REVERT: A 673 MET cc_start: 0.9142 (tpp) cc_final: 0.8774 (tpp) REVERT: A 988 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8291 (t70) REVERT: A 989 TYR cc_start: 0.7628 (t80) cc_final: 0.7360 (t80) outliers start: 36 outliers final: 29 residues processed: 119 average time/residue: 0.1687 time to fit residues: 30.9127 Evaluate side-chains 125 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 667 TYR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 800 TYR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain A residue 1308 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.115547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.093277 restraints weight = 33145.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.095520 restraints weight = 20656.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.097033 restraints weight = 15104.628| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9887 Z= 0.212 Angle : 0.764 10.286 13447 Z= 0.364 Chirality : 0.050 0.440 1590 Planarity : 0.005 0.119 1717 Dihedral : 13.105 94.439 1572 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.70 % Favored : 88.98 % Rotamer: Outliers : 3.46 % Allowed : 20.96 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.24), residues: 1234 helix: 0.57 (0.38), residues: 196 sheet: -1.19 (0.25), residues: 437 loop : -2.73 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1069 HIS 0.005 0.001 HIS A1062 PHE 0.029 0.002 PHE A 130 TYR 0.025 0.001 TYR A 970 ARG 0.007 0.000 ARG A 787 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.43 seconds wall clock time: 33 minutes 46.56 seconds (2026.56 seconds total)