Starting phenix.real_space_refine on Sun Aug 24 01:24:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.map" model { file = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpq_38559/08_2025/8xpq_38559.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 10334 2.51 5 N 2682 2.21 5 O 2864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 7983 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 34, 'TRANS': 1004} Chain breaks: 6 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 107 Restraints were copied for chains: B Time building chain proxies: 8.55, per 1000 atoms: 0.54 Number of scatterers: 15966 At special positions: 0 Unit cell: (104.76, 132.84, 124.2, 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 86 16.00 O 2864 8.00 N 2682 7.00 C 10334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 710.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3916 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 73.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.305A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.893A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.739A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.537A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.748A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.646A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.969A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 379 removed outlier: 4.076A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.643A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.355A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 571 through 600 removed outlier: 3.846A pdb=" N ALA A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 653 removed outlier: 4.484A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 691 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.800A pdb=" N ILE A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 752 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'A' and resid 803 through 853 Proline residue: A 819 - end of helix removed outlier: 3.656A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.942A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.548A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.676A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1122 Processing helix chain 'A' and resid 1206 through 1210 removed outlier: 4.155A pdb=" N SER A1210 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.305A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.894A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.739A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.537A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 253 removed outlier: 3.747A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 292 Proline residue: B 276 - end of helix removed outlier: 3.646A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 removed outlier: 3.969A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 376 through 379 removed outlier: 4.076A pdb=" N ALA B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 381 through 412 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.643A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.355A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 547 through 559 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 571 through 600 removed outlier: 3.847A pdb=" N ALA B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 639 through 653 removed outlier: 4.484A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 691 through 699 removed outlier: 3.800A pdb=" N ILE B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 752 Processing helix chain 'B' and resid 763 through 776 Processing helix chain 'B' and resid 803 through 853 Proline residue: B 819 - end of helix removed outlier: 3.657A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.942A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.548A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.676A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1069 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1122 Processing helix chain 'B' and resid 1206 through 1210 removed outlier: 4.155A pdb=" N SER B1210 " --> pdb=" O SER B1207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.270A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.647A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.430A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL A1145 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A1165 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'A' and resid 1203 through 1204 removed outlier: 3.855A pdb=" N SER A1213 " --> pdb=" O ASP A1204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 982 removed outlier: 6.270A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.647A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1126 removed outlier: 6.429A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B1145 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B1165 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1137 Processing sheet with id=AB1, first strand: chain 'B' and resid 1203 through 1204 removed outlier: 3.855A pdb=" N SER B1213 " --> pdb=" O ASP B1204 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3534 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: 3.17 Time building geometry restraints manager: 1.70 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: 5081 1.34 - 1.46: 2746 1.46 - 1.58: 8273 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 16254 Sorted by residual: bond pdb=" N CYS B 559 " pdb=" CA CYS B 559 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.19e-02 7.06e+03 6.55e+00 bond pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.19e-02 7.06e+03 5.97e+00 bond pdb=" CA CYS A 559 " pdb=" C CYS A 559 " ideal model delta sigma weight residual 1.525 1.549 -0.025 1.04e-02 9.25e+03 5.68e+00 bond pdb=" CA CYS B 559 " pdb=" C CYS B 559 " ideal model delta sigma weight residual 1.525 1.549 -0.024 1.04e-02 9.25e+03 5.40e+00 bond pdb=" CA ILE A1198 " pdb=" C ILE A1198 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.27e-02 6.20e+03 4.69e+00 ... (remaining 16249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 21232 1.76 - 3.53: 651 3.53 - 5.29: 125 5.29 - 7.05: 34 7.05 - 8.82: 20 Bond angle restraints: 22062 Sorted by residual: angle pdb=" N PRO A1197 " pdb=" CA PRO A1197 " pdb=" C PRO A1197 " ideal model delta sigma weight residual 114.03 105.35 8.68 1.23e+00 6.61e-01 4.98e+01 angle pdb=" N PRO B1197 " pdb=" CA PRO B1197 " pdb=" C PRO B1197 " ideal model delta sigma weight residual 114.03 105.36 8.67 1.23e+00 6.61e-01 4.97e+01 angle pdb=" C HIS B1156 " pdb=" N THR B1157 " pdb=" CA THR B1157 " ideal model delta sigma weight residual 122.46 129.86 -7.40 1.41e+00 5.03e-01 2.76e+01 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 122.46 129.85 -7.39 1.41e+00 5.03e-01 2.75e+01 angle pdb=" C VAL A 558 " pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 123.46 117.49 5.97 1.35e+00 5.49e-01 1.96e+01 ... (remaining 22057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 8939 17.44 - 34.88: 627 34.88 - 52.32: 158 52.32 - 69.76: 30 69.76 - 87.20: 4 Dihedral angle restraints: 9758 sinusoidal: 3726 harmonic: 6032 Sorted by residual: dihedral pdb=" CA ARG A1190 " pdb=" C ARG A1190 " pdb=" N ASN A1191 " pdb=" CA ASN A1191 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ARG B1190 " pdb=" C ARG B1190 " pdb=" N ASN B1191 " pdb=" CA ASN B1191 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 9755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2451 0.088 - 0.177: 199 0.177 - 0.265: 8 0.265 - 0.354: 0 0.354 - 0.442: 2 Chirality restraints: 2660 Sorted by residual: chirality pdb=" CA LEU B1199 " pdb=" N LEU B1199 " pdb=" C LEU B1199 " pdb=" CB LEU B1199 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LEU A1199 " pdb=" N LEU A1199 " pdb=" C LEU A1199 " pdb=" CB LEU A1199 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2657 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C LEU B 467 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 467 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 468 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C LEU A 467 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 467 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 468 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 952 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO B 953 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 953 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 953 " -0.035 5.00e-02 4.00e+02 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4314 2.81 - 3.33: 15352 3.33 - 3.85: 26781 3.85 - 4.38: 29506 4.38 - 4.90: 53178 Nonbonded interactions: 129131 Sorted by model distance: nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.286 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.286 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.321 3.040 nonbonded pdb=" O ILE B 469 " pdb=" OG1 THR B 473 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN B1177 " pdb=" OG1 THR B1179 " model vdw 2.329 3.040 ... (remaining 129126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.006 0.081 16254 Z= 0.269 Angle : 0.799 8.817 22062 Z= 0.451 Chirality : 0.052 0.442 2660 Planarity : 0.007 0.064 2752 Dihedral : 13.261 87.203 5842 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 5.24 % Allowed : 9.18 % Favored : 85.58 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.16), residues: 2050 helix: -0.61 (0.12), residues: 1410 sheet: -0.94 (0.54), residues: 92 loop : -2.36 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.012 0.002 TYR B 102 PHE 0.015 0.002 PHE A 352 TRP 0.022 0.002 TRP B 962 HIS 0.007 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00581 (16254) covalent geometry : angle 0.79876 (22062) hydrogen bonds : bond 0.11687 ( 1198) hydrogen bonds : angle 5.86608 ( 3534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 561 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6922 (tp30) cc_final: 0.6347 (tp30) REVERT: A 154 MET cc_start: 0.7462 (tpp) cc_final: 0.7151 (mmm) REVERT: A 160 MET cc_start: 0.6575 (mmt) cc_final: 0.6307 (mmm) REVERT: A 248 PHE cc_start: 0.7219 (m-80) cc_final: 0.7018 (m-10) REVERT: A 321 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7321 (t) REVERT: A 337 GLU cc_start: 0.7774 (mp0) cc_final: 0.7448 (mp0) REVERT: A 366 MET cc_start: 0.8577 (mmm) cc_final: 0.8323 (mmm) REVERT: A 368 VAL cc_start: 0.7885 (t) cc_final: 0.7644 (p) REVERT: A 375 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7898 (mtmm) REVERT: A 494 MET cc_start: 0.8075 (tpp) cc_final: 0.7769 (tpp) REVERT: A 552 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (tp) REVERT: A 820 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7630 (mmmt) REVERT: A 823 LEU cc_start: 0.7975 (mp) cc_final: 0.7682 (mm) REVERT: A 847 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 849 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 928 HIS cc_start: 0.7543 (t-90) cc_final: 0.7340 (t-170) REVERT: A 931 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 973 ILE cc_start: 0.8656 (mm) cc_final: 0.8351 (tt) REVERT: A 987 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8562 (m) REVERT: A 993 ASP cc_start: 0.7999 (p0) cc_final: 0.7777 (p0) REVERT: A 994 GLU cc_start: 0.8185 (mp0) cc_final: 0.7876 (mp0) REVERT: A 1061 THR cc_start: 0.8316 (p) cc_final: 0.8073 (p) REVERT: A 1073 MET cc_start: 0.8579 (mmm) cc_final: 0.8113 (mmm) REVERT: A 1087 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 1094 VAL cc_start: 0.8695 (m) cc_final: 0.8364 (p) REVERT: A 1098 ILE cc_start: 0.8972 (tt) cc_final: 0.8670 (tt) REVERT: A 1122 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7176 (mm-30) REVERT: A 1131 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 1134 PHE cc_start: 0.8007 (m-80) cc_final: 0.7762 (m-10) REVERT: A 1142 LEU cc_start: 0.7806 (mp) cc_final: 0.7534 (mm) REVERT: A 1147 LEU cc_start: 0.7482 (tp) cc_final: 0.7119 (tp) REVERT: A 1166 LEU cc_start: 0.8604 (tp) cc_final: 0.8277 (tp) REVERT: A 1202 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6719 (ttt-90) REVERT: A 1215 THR cc_start: 0.8024 (p) cc_final: 0.7754 (p) REVERT: B 124 GLU cc_start: 0.6710 (tp30) cc_final: 0.6171 (tp30) REVERT: B 149 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 154 MET cc_start: 0.7610 (tpp) cc_final: 0.7276 (mmm) REVERT: B 160 MET cc_start: 0.6562 (mmt) cc_final: 0.6208 (mmm) REVERT: B 220 LEU cc_start: 0.8194 (mt) cc_final: 0.7935 (mt) REVERT: B 321 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 366 MET cc_start: 0.8460 (mmm) cc_final: 0.8211 (mmm) REVERT: B 375 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8135 (ttmm) REVERT: B 380 VAL cc_start: 0.7197 (p) cc_final: 0.6915 (p) REVERT: B 520 ASP cc_start: 0.7341 (p0) cc_final: 0.7138 (p0) REVERT: B 534 ASP cc_start: 0.6994 (t70) cc_final: 0.6746 (t0) REVERT: B 556 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7985 (mmmt) REVERT: B 569 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8319 (mp0) REVERT: B 621 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: B 820 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7737 (mmmt) REVERT: B 823 LEU cc_start: 0.8007 (mp) cc_final: 0.7721 (mm) REVERT: B 841 LYS cc_start: 0.7963 (mtpm) cc_final: 0.7729 (mtpm) REVERT: B 847 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 849 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 942 MET cc_start: 0.8308 (tpp) cc_final: 0.8078 (tpp) REVERT: B 971 ASP cc_start: 0.8272 (m-30) cc_final: 0.7893 (m-30) REVERT: B 972 PHE cc_start: 0.7868 (t80) cc_final: 0.7662 (t80) REVERT: B 973 ILE cc_start: 0.8453 (mm) cc_final: 0.8205 (tt) REVERT: B 986 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 993 ASP cc_start: 0.8082 (p0) cc_final: 0.7834 (p0) REVERT: B 994 GLU cc_start: 0.8091 (mp0) cc_final: 0.7814 (mp0) REVERT: B 1044 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 1072 ASP cc_start: 0.7591 (m-30) cc_final: 0.7373 (m-30) REVERT: B 1073 MET cc_start: 0.8489 (mmm) cc_final: 0.8187 (mmm) REVERT: B 1094 VAL cc_start: 0.8689 (m) cc_final: 0.8396 (p) REVERT: B 1098 ILE cc_start: 0.8958 (tt) cc_final: 0.8679 (tt) REVERT: B 1105 GLU cc_start: 0.7925 (tt0) cc_final: 0.7723 (tt0) REVERT: B 1110 GLN cc_start: 0.8422 (mp10) cc_final: 0.8188 (mp10) REVERT: B 1122 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 1127 VAL cc_start: 0.7823 (t) cc_final: 0.7482 (m) REVERT: B 1134 PHE cc_start: 0.8062 (m-80) cc_final: 0.7801 (m-80) REVERT: B 1138 ILE cc_start: 0.8451 (mt) cc_final: 0.8187 (mt) REVERT: B 1172 HIS cc_start: 0.7827 (t-170) cc_final: 0.7545 (t-170) REVERT: B 1188 VAL cc_start: 0.8748 (m) cc_final: 0.8522 (p) outliers start: 88 outliers final: 32 residues processed: 622 average time/residue: 0.1298 time to fit residues: 118.5918 Evaluate side-chains 520 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 483 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 559 CYS Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 600 HIS A 614 HIS A 832 GLN A 886 GLN A 917 GLN A 955 ASN A1106 GLN A1114 GLN A1120 HIS B 165 GLN B 292 HIS B 600 HIS B 614 HIS B 624 GLN ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 GLN B 886 GLN B 917 GLN B 955 ASN B1149 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132441 restraints weight = 25420.304| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.35 r_work: 0.3614 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16254 Z= 0.170 Angle : 0.632 7.364 22062 Z= 0.330 Chirality : 0.042 0.149 2660 Planarity : 0.005 0.051 2752 Dihedral : 6.675 59.511 2281 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.13 % Allowed : 16.27 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.18), residues: 2050 helix: 0.96 (0.13), residues: 1438 sheet: 0.08 (0.58), residues: 96 loop : -2.02 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 499 TYR 0.012 0.001 TYR B 837 PHE 0.015 0.002 PHE A 455 TRP 0.014 0.002 TRP B1091 HIS 0.007 0.001 HIS B1172 Details of bonding type rmsd covalent geometry : bond 0.00367 (16254) covalent geometry : angle 0.63171 (22062) hydrogen bonds : bond 0.04838 ( 1198) hydrogen bonds : angle 4.39362 ( 3534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 525 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6825 (tp30) cc_final: 0.6439 (tp30) REVERT: A 149 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7176 (tm-30) REVERT: A 154 MET cc_start: 0.7832 (tpp) cc_final: 0.7430 (tpp) REVERT: A 155 ASP cc_start: 0.7537 (t70) cc_final: 0.7301 (t70) REVERT: A 160 MET cc_start: 0.7128 (mmt) cc_final: 0.6784 (mmm) REVERT: A 186 MET cc_start: 0.7378 (mtp) cc_final: 0.7145 (mmm) REVERT: A 187 ASN cc_start: 0.7191 (m-40) cc_final: 0.6840 (m110) REVERT: A 248 PHE cc_start: 0.7977 (m-80) cc_final: 0.7765 (m-80) REVERT: A 265 VAL cc_start: 0.8090 (t) cc_final: 0.7820 (p) REVERT: A 289 PHE cc_start: 0.7793 (t80) cc_final: 0.7435 (t80) REVERT: A 300 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 316 ASP cc_start: 0.7558 (t0) cc_final: 0.7353 (m-30) REVERT: A 337 GLU cc_start: 0.7656 (mp0) cc_final: 0.7323 (mp0) REVERT: A 355 MET cc_start: 0.8193 (ttp) cc_final: 0.7871 (ttp) REVERT: A 375 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8246 (ttmm) REVERT: A 404 SER cc_start: 0.7972 (m) cc_final: 0.7769 (p) REVERT: A 427 TRP cc_start: 0.8206 (t-100) cc_final: 0.7683 (t-100) REVERT: A 511 MET cc_start: 0.8400 (ttt) cc_final: 0.8021 (ttp) REVERT: A 534 ASP cc_start: 0.7418 (t70) cc_final: 0.7176 (t0) REVERT: A 536 TYR cc_start: 0.7835 (m-80) cc_final: 0.7360 (m-10) REVERT: A 552 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7454 (tt) REVERT: A 578 MET cc_start: 0.7221 (mtm) cc_final: 0.6879 (mtp) REVERT: A 823 LEU cc_start: 0.8253 (mp) cc_final: 0.7923 (mm) REVERT: A 845 ILE cc_start: 0.8645 (mt) cc_final: 0.8385 (mm) REVERT: A 847 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 849 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 887 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7721 (ttt90) REVERT: A 926 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 971 ASP cc_start: 0.8194 (m-30) cc_final: 0.7799 (m-30) REVERT: A 987 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 993 ASP cc_start: 0.7745 (p0) cc_final: 0.7401 (p0) REVERT: A 996 ASP cc_start: 0.7558 (p0) cc_final: 0.7272 (p0) REVERT: A 1002 VAL cc_start: 0.8403 (m) cc_final: 0.8166 (p) REVERT: A 1044 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 1061 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 1073 MET cc_start: 0.8554 (mmm) cc_final: 0.8122 (mmm) REVERT: A 1098 ILE cc_start: 0.8987 (tt) cc_final: 0.8663 (tt) REVERT: A 1104 MET cc_start: 0.7865 (tpp) cc_final: 0.7496 (tpp) REVERT: A 1122 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 1134 PHE cc_start: 0.7952 (m-80) cc_final: 0.7737 (m-10) REVERT: A 1190 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.7039 (ttm-80) REVERT: B 124 GLU cc_start: 0.6525 (tp30) cc_final: 0.6211 (tp30) REVERT: B 140 GLN cc_start: 0.8004 (mm110) cc_final: 0.7684 (mp10) REVERT: B 154 MET cc_start: 0.7995 (tpp) cc_final: 0.7503 (tpp) REVERT: B 155 ASP cc_start: 0.7452 (t70) cc_final: 0.7224 (t70) REVERT: B 160 MET cc_start: 0.6994 (mmt) cc_final: 0.6660 (mmm) REVERT: B 176 VAL cc_start: 0.7917 (p) cc_final: 0.7709 (p) REVERT: B 231 GLU cc_start: 0.7166 (tt0) cc_final: 0.6820 (mt-10) REVERT: B 265 VAL cc_start: 0.7987 (t) cc_final: 0.7744 (p) REVERT: B 319 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7951 (mt) REVERT: B 333 ILE cc_start: 0.8039 (mt) cc_final: 0.7499 (mm) REVERT: B 337 GLU cc_start: 0.7692 (mp0) cc_final: 0.7159 (mp0) REVERT: B 375 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8235 (mtmm) REVERT: B 401 MET cc_start: 0.7333 (mmp) cc_final: 0.7008 (mtp) REVERT: B 404 SER cc_start: 0.7660 (m) cc_final: 0.7458 (p) REVERT: B 490 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7320 (tttp) REVERT: B 534 ASP cc_start: 0.7516 (t70) cc_final: 0.7187 (t0) REVERT: B 565 MET cc_start: 0.4712 (ppp) cc_final: 0.4444 (ppp) REVERT: B 569 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8097 (mp0) REVERT: B 578 MET cc_start: 0.7352 (mtt) cc_final: 0.7041 (mtp) REVERT: B 595 TRP cc_start: 0.8284 (m100) cc_final: 0.7982 (m100) REVERT: B 605 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8155 (tpp80) REVERT: B 624 GLN cc_start: 0.7530 (pt0) cc_final: 0.7282 (pt0) REVERT: B 820 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7664 (mmmt) REVERT: B 823 LEU cc_start: 0.8266 (mp) cc_final: 0.8012 (mm) REVERT: B 832 GLN cc_start: 0.8234 (tp40) cc_final: 0.7940 (tm-30) REVERT: B 841 LYS cc_start: 0.7818 (mtpm) cc_final: 0.7596 (mtpm) REVERT: B 847 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6969 (mm-30) REVERT: B 898 THR cc_start: 0.8300 (m) cc_final: 0.8079 (p) REVERT: B 926 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7306 (mm-30) REVERT: B 971 ASP cc_start: 0.8259 (m-30) cc_final: 0.7882 (m-30) REVERT: B 973 ILE cc_start: 0.8599 (mm) cc_final: 0.8198 (tt) REVERT: B 983 ASP cc_start: 0.8130 (p0) cc_final: 0.7805 (p0) REVERT: B 987 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8665 (m) REVERT: B 991 GLU cc_start: 0.7697 (tt0) cc_final: 0.7492 (tt0) REVERT: B 994 GLU cc_start: 0.8003 (mp0) cc_final: 0.7742 (mp0) REVERT: B 996 ASP cc_start: 0.7708 (p0) cc_final: 0.7466 (p0) REVERT: B 1037 THR cc_start: 0.7958 (t) cc_final: 0.7738 (p) REVERT: B 1051 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: B 1094 VAL cc_start: 0.8491 (m) cc_final: 0.8223 (p) REVERT: B 1098 ILE cc_start: 0.9007 (tt) cc_final: 0.8657 (tt) REVERT: B 1104 MET cc_start: 0.7808 (tpp) cc_final: 0.7416 (mmm) REVERT: B 1105 GLU cc_start: 0.7769 (tt0) cc_final: 0.7531 (tt0) REVERT: B 1110 GLN cc_start: 0.8348 (mp10) cc_final: 0.8020 (mp10) REVERT: B 1122 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7243 (mm-30) REVERT: B 1128 ASP cc_start: 0.7160 (t0) cc_final: 0.6877 (t70) REVERT: B 1134 PHE cc_start: 0.8068 (m-80) cc_final: 0.7786 (m-10) REVERT: B 1172 HIS cc_start: 0.7492 (t-170) cc_final: 0.7120 (t-170) REVERT: B 1188 VAL cc_start: 0.8667 (m) cc_final: 0.8303 (p) outliers start: 86 outliers final: 53 residues processed: 572 average time/residue: 0.1238 time to fit residues: 105.2974 Evaluate side-chains 537 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 478 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1165 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1051 LYS Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 TRP Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1135 GLN Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 113 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 165 GLN A 374 GLN A 600 HIS A 614 HIS ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1177 GLN B 165 GLN B 614 HIS ** B 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B1137 ASN B1149 ASN B1177 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127372 restraints weight = 25254.154| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.32 r_work: 0.3543 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16254 Z= 0.143 Angle : 0.573 6.374 22062 Z= 0.303 Chirality : 0.041 0.176 2660 Planarity : 0.004 0.040 2752 Dihedral : 5.736 59.110 2254 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.42 % Allowed : 18.06 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 2050 helix: 1.55 (0.14), residues: 1430 sheet: 0.58 (0.59), residues: 96 loop : -1.88 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.012 0.001 TYR A1125 PHE 0.012 0.001 PHE A 999 TRP 0.012 0.002 TRP B 962 HIS 0.005 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00300 (16254) covalent geometry : angle 0.57327 (22062) hydrogen bonds : bond 0.04496 ( 1198) hydrogen bonds : angle 4.15668 ( 3534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 526 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (t) REVERT: A 124 GLU cc_start: 0.6822 (tp30) cc_final: 0.6431 (tp30) REVERT: A 140 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7992 (mp10) REVERT: A 149 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 154 MET cc_start: 0.7986 (tpp) cc_final: 0.7764 (tpp) REVERT: A 155 ASP cc_start: 0.7649 (t70) cc_final: 0.7410 (t70) REVERT: A 166 VAL cc_start: 0.7483 (t) cc_final: 0.7226 (t) REVERT: A 180 LEU cc_start: 0.8254 (tt) cc_final: 0.8026 (tp) REVERT: A 186 MET cc_start: 0.7414 (mtp) cc_final: 0.7103 (mtp) REVERT: A 187 ASN cc_start: 0.7281 (m-40) cc_final: 0.6801 (m-40) REVERT: A 265 VAL cc_start: 0.8206 (t) cc_final: 0.7980 (p) REVERT: A 289 PHE cc_start: 0.7903 (t80) cc_final: 0.7557 (t80) REVERT: A 296 ASP cc_start: 0.7601 (p0) cc_final: 0.7217 (p0) REVERT: A 337 GLU cc_start: 0.7680 (mp0) cc_final: 0.7334 (mp0) REVERT: A 346 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 355 MET cc_start: 0.8209 (ttp) cc_final: 0.7878 (ttp) REVERT: A 427 TRP cc_start: 0.8515 (t-100) cc_final: 0.7685 (t-100) REVERT: A 477 LEU cc_start: 0.8196 (mm) cc_final: 0.7912 (mp) REVERT: A 511 MET cc_start: 0.8394 (ttt) cc_final: 0.8128 (ttt) REVERT: A 534 ASP cc_start: 0.7602 (t70) cc_final: 0.7386 (t0) REVERT: A 536 TYR cc_start: 0.8030 (m-80) cc_final: 0.7815 (m-10) REVERT: A 552 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7522 (tt) REVERT: A 599 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: A 624 GLN cc_start: 0.7623 (pt0) cc_final: 0.7323 (pp30) REVERT: A 632 LYS cc_start: 0.7767 (mtpm) cc_final: 0.7532 (mtpp) REVERT: A 820 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7757 (mmmt) REVERT: A 823 LEU cc_start: 0.8336 (mp) cc_final: 0.8020 (mm) REVERT: A 832 GLN cc_start: 0.8243 (tp40) cc_final: 0.8022 (tm-30) REVERT: A 958 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8111 (ttpp) REVERT: A 971 ASP cc_start: 0.8204 (m-30) cc_final: 0.7855 (m-30) REVERT: A 987 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 991 GLU cc_start: 0.7619 (tt0) cc_final: 0.7387 (tt0) REVERT: A 993 ASP cc_start: 0.7809 (p0) cc_final: 0.7526 (p0) REVERT: A 994 GLU cc_start: 0.7915 (mp0) cc_final: 0.7686 (mp0) REVERT: A 1044 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 1061 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 1067 PHE cc_start: 0.7855 (t80) cc_final: 0.7425 (t80) REVERT: A 1073 MET cc_start: 0.8479 (mmm) cc_final: 0.8050 (mmm) REVERT: A 1094 VAL cc_start: 0.8512 (m) cc_final: 0.8202 (p) REVERT: A 1098 ILE cc_start: 0.8987 (tt) cc_final: 0.8667 (tt) REVERT: A 1122 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 1125 TYR cc_start: 0.8089 (p90) cc_final: 0.7826 (p90) REVERT: A 1127 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8120 (p) REVERT: A 1134 PHE cc_start: 0.8032 (m-80) cc_final: 0.7626 (m-10) REVERT: A 1190 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6786 (ttm-80) REVERT: B 79 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 140 GLN cc_start: 0.8026 (mm110) cc_final: 0.7788 (mp10) REVERT: B 149 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7248 (tp30) REVERT: B 154 MET cc_start: 0.8204 (tpp) cc_final: 0.7557 (tpp) REVERT: B 155 ASP cc_start: 0.7524 (t70) cc_final: 0.7290 (t70) REVERT: B 160 MET cc_start: 0.7129 (mmt) cc_final: 0.6793 (mmm) REVERT: B 206 SER cc_start: 0.8120 (t) cc_final: 0.7829 (t) REVERT: B 231 GLU cc_start: 0.7283 (tt0) cc_final: 0.6928 (mt-10) REVERT: B 289 PHE cc_start: 0.7871 (t80) cc_final: 0.7496 (t80) REVERT: B 319 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 375 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8299 (ttpp) REVERT: B 401 MET cc_start: 0.7519 (mmp) cc_final: 0.7293 (mtp) REVERT: B 520 ASP cc_start: 0.7721 (p0) cc_final: 0.7454 (p0) REVERT: B 534 ASP cc_start: 0.7646 (t70) cc_final: 0.7354 (t0) REVERT: B 565 MET cc_start: 0.4907 (ppp) cc_final: 0.4475 (ppp) REVERT: B 578 MET cc_start: 0.7579 (mtt) cc_final: 0.7188 (mtp) REVERT: B 595 TRP cc_start: 0.8418 (m100) cc_final: 0.8110 (m100) REVERT: B 596 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7970 (ttmm) REVERT: B 599 GLU cc_start: 0.7746 (tp30) cc_final: 0.7535 (mm-30) REVERT: B 600 HIS cc_start: 0.8137 (m90) cc_final: 0.7893 (m-70) REVERT: B 823 LEU cc_start: 0.8312 (mp) cc_final: 0.8036 (mm) REVERT: B 832 GLN cc_start: 0.8302 (tp40) cc_final: 0.8035 (tm-30) REVERT: B 853 ILE cc_start: 0.8394 (mm) cc_final: 0.7921 (tp) REVERT: B 897 LYS cc_start: 0.8295 (mmtp) cc_final: 0.8094 (mttp) REVERT: B 898 THR cc_start: 0.8472 (m) cc_final: 0.8161 (p) REVERT: B 926 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 929 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7834 (ttmt) REVERT: B 971 ASP cc_start: 0.8194 (m-30) cc_final: 0.7827 (m-30) REVERT: B 972 PHE cc_start: 0.8078 (t80) cc_final: 0.7843 (t80) REVERT: B 987 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8737 (m) REVERT: B 1002 VAL cc_start: 0.8460 (m) cc_final: 0.8105 (p) REVERT: B 1061 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 1067 PHE cc_start: 0.7774 (t80) cc_final: 0.7308 (t80) REVERT: B 1094 VAL cc_start: 0.8456 (m) cc_final: 0.8223 (p) REVERT: B 1098 ILE cc_start: 0.9039 (tt) cc_final: 0.8679 (tt) REVERT: B 1104 MET cc_start: 0.7718 (tpp) cc_final: 0.7418 (tpp) REVERT: B 1110 GLN cc_start: 0.8341 (mp10) cc_final: 0.8085 (mp10) REVERT: B 1117 VAL cc_start: 0.8837 (t) cc_final: 0.8490 (t) REVERT: B 1127 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8021 (m) REVERT: B 1128 ASP cc_start: 0.7272 (t0) cc_final: 0.7045 (t0) REVERT: B 1134 PHE cc_start: 0.8090 (m-80) cc_final: 0.7610 (m-10) REVERT: B 1141 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 1172 HIS cc_start: 0.7432 (t-170) cc_final: 0.7123 (t-170) REVERT: B 1214 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.6922 (mm) outliers start: 91 outliers final: 52 residues processed: 568 average time/residue: 0.1204 time to fit residues: 100.0029 Evaluate side-chains 558 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 492 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 935 GLU Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 968 LYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1069 THR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1149 ASN Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1165 CYS Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1214 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1392 > 50: distance: 8 - 12: 12.790 distance: 12 - 13: 6.392 distance: 13 - 14: 23.624 distance: 13 - 16: 26.533 distance: 14 - 15: 41.176 distance: 14 - 20: 33.512 distance: 16 - 17: 18.199 distance: 17 - 18: 27.297 distance: 18 - 19: 18.738 distance: 20 - 21: 32.853 distance: 21 - 22: 49.081 distance: 21 - 24: 49.781 distance: 22 - 23: 32.805 distance: 22 - 28: 58.754 distance: 23 - 52: 49.785 distance: 24 - 25: 22.948 distance: 25 - 26: 39.044 distance: 25 - 27: 24.465 distance: 28 - 29: 52.332 distance: 28 - 34: 26.100 distance: 29 - 30: 28.992 distance: 29 - 32: 56.003 distance: 30 - 31: 32.620 distance: 30 - 35: 34.823 distance: 31 - 60: 36.410 distance: 32 - 33: 20.795 distance: 33 - 34: 41.903 distance: 35 - 36: 33.643 distance: 36 - 37: 46.843 distance: 36 - 39: 40.716 distance: 37 - 38: 39.989 distance: 37 - 45: 46.066 distance: 38 - 68: 61.002 distance: 39 - 40: 36.921 distance: 40 - 41: 30.669 distance: 40 - 42: 45.496 distance: 41 - 43: 15.806 distance: 42 - 44: 4.250 distance: 43 - 44: 23.229 distance: 45 - 46: 21.876 distance: 46 - 47: 42.390 distance: 46 - 49: 37.557 distance: 47 - 48: 3.667 distance: 47 - 52: 42.869 distance: 48 - 77: 61.845 distance: 49 - 50: 50.981 distance: 49 - 51: 48.992 distance: 52 - 53: 21.238 distance: 53 - 54: 15.792 distance: 53 - 56: 29.569 distance: 54 - 55: 8.884 distance: 54 - 60: 22.986 distance: 55 - 85: 36.516 distance: 56 - 57: 32.362 distance: 57 - 58: 44.139 distance: 57 - 59: 35.935 distance: 60 - 61: 40.806 distance: 61 - 62: 19.333 distance: 61 - 64: 20.158 distance: 62 - 63: 39.816 distance: 62 - 68: 49.361 distance: 63 - 96: 28.010 distance: 64 - 65: 43.768 distance: 65 - 66: 37.054 distance: 65 - 67: 29.975 distance: 68 - 69: 4.705 distance: 69 - 70: 21.621 distance: 69 - 72: 19.503 distance: 70 - 71: 41.450 distance: 70 - 77: 12.910 distance: 72 - 73: 27.176 distance: 73 - 74: 32.531 distance: 74 - 75: 14.898 distance: 74 - 76: 19.409 distance: 77 - 78: 13.488 distance: 78 - 79: 61.778 distance: 78 - 81: 42.913 distance: 79 - 80: 39.736 distance: 79 - 85: 40.397 distance: 81 - 82: 45.724 distance: 81 - 83: 51.962 distance: 82 - 84: 22.325 distance: 85 - 86: 38.744 distance: 86 - 87: 60.602 distance: 86 - 89: 53.038 distance: 87 - 88: 24.952 distance: 87 - 96: 28.358 distance: 89 - 90: 18.809 distance: 90 - 91: 39.961 distance: 90 - 92: 34.197 distance: 91 - 93: 8.200 distance: 92 - 94: 19.370 distance: 93 - 95: 10.462 distance: 94 - 95: 13.646 distance: 179 - 188: 3.096