Starting phenix.real_space_refine on Fri Aug 22 22:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2025/9bfp_44502.cif" } resolution = 2.78 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= -0.001 sd= 0.046 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 34 5.16 5 C 5251 2.51 5 N 1447 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s 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: 8263 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8207 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 961} Chain breaks: 5 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Time building chain proxies: 1.59, per 1000 atoms: 0.19 Number of scatterers: 8263 At special positions: 0 Unit cell: (79.68, 86.32, 163.51, 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 34 16.00 O 1531 8.00 N 1447 7.00 C 5251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A2601 " - " ASN A 505 " " NAG A2602 " - " ASN A1228 " " NAG B 1 " - " ASN A 966 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 414.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 8.6% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.510A pdb=" N ARG A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.717A pdb=" N ARG A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 312 removed outlier: 3.823A pdb=" N ILE A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.878A pdb=" N ALA A1070 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.692A pdb=" N SER A1176 " --> pdb=" O ASP A1173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.978A pdb=" N LEU A 329 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 450 removed outlier: 5.052A pdb=" N ILE A 443 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS A 459 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 488 removed outlier: 3.570A pdb=" N GLY A 524 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568 removed outlier: 7.014A pdb=" N VAL A 552 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 810 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 573 through 576 removed outlier: 7.026A pdb=" N LEU A 588 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS A 598 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU A 600 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 605 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 631 removed outlier: 6.577A pdb=" N ALA A 640 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 628 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR A 638 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 630 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 636 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 652 " --> pdb=" O MET A 641 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 624 through 631 removed outlier: 6.577A pdb=" N ALA A 640 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 628 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR A 638 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 630 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 636 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 654 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 676 through 680 removed outlier: 3.746A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 688 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 694 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.528A pdb=" N ILE A 724 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.753A pdb=" N ALA A 798 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 832 through 835 Processing sheet with id=AB5, first strand: chain 'A' and resid 875 through 881 removed outlier: 5.852A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 949 through 954 removed outlier: 5.284A pdb=" N VAL A 938 " --> pdb=" O GLN A 951 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 939 " --> pdb=" O TRP A 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1180 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 963 through 964 removed outlier: 3.530A pdb=" N TYR A 972 " --> pdb=" O HIS A 980 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.773A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 6.581A pdb=" N LEU A1060 " --> pdb=" O TYR A1073 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1089 removed outlier: 6.607A pdb=" N LEU A1098 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A1086 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A1096 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A1088 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN A1094 " --> pdb=" O LEU A1088 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP A1097 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A1104 " --> pdb=" O GLY A1101 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A1105 " --> pdb=" O GLN A1124 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A1124 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A1107 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1137 through 1139 Processing sheet with id=AC3, first strand: chain 'A' and resid 1207 through 1209 removed outlier: 4.513A pdb=" N HIS A1217 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A1218 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1243 through 1248 279 hydrogen bonds defined for protein. 714 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: 1.80 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2631 1.34 - 1.46: 2043 1.46 - 1.59: 3756 1.59 - 1.72: 0 1.72 - 1.84: 52 Bond restraints: 8482 Sorted by residual: bond pdb=" N ASN A 905 " pdb=" CA ASN A 905 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" N VAL A 420 " pdb=" CA VAL A 420 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.27e-02 6.20e+03 7.53e+00 bond pdb=" N VAL A 906 " pdb=" CA VAL A 906 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.21e+00 bond pdb=" CA SER A 862 " pdb=" CB SER A 862 " ideal model delta sigma weight residual 1.530 1.490 0.041 1.52e-02 4.33e+03 7.16e+00 bond pdb=" CA SER A 860 " pdb=" CB SER A 860 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.35e-02 5.49e+03 6.97e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 11242 3.38 - 6.77: 255 6.77 - 10.15: 40 10.15 - 13.53: 8 13.53 - 16.92: 1 Bond angle restraints: 11546 Sorted by residual: angle pdb=" C PHE A 413 " pdb=" CA PHE A 413 " pdb=" CB PHE A 413 " ideal model delta sigma weight residual 110.85 119.75 -8.90 1.70e+00 3.46e-01 2.74e+01 angle pdb=" C SER A 823 " pdb=" N ALA A 824 " pdb=" CA ALA A 824 " ideal model delta sigma weight residual 123.05 130.89 -7.84 1.57e+00 4.06e-01 2.49e+01 angle pdb=" C ASN A 690 " pdb=" N GLU A 691 " pdb=" CA GLU A 691 " ideal model delta sigma weight residual 120.28 127.34 -7.06 1.44e+00 4.82e-01 2.40e+01 angle pdb=" OG1 THR A1273 " pdb=" CB THR A1273 " pdb=" CG2 THR A1273 " ideal model delta sigma weight residual 109.30 99.59 9.71 2.00e+00 2.50e-01 2.36e+01 angle pdb=" C THR A 464 " pdb=" N ASN A 465 " pdb=" CA ASN A 465 " ideal model delta sigma weight residual 122.19 129.03 -6.84 1.41e+00 5.03e-01 2.36e+01 ... (remaining 11541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4721 17.97 - 35.93: 332 35.93 - 53.90: 59 53.90 - 71.87: 15 71.87 - 89.83: 8 Dihedral angle restraints: 5135 sinusoidal: 2150 harmonic: 2985 Sorted by residual: dihedral pdb=" CB CYS A 981 " pdb=" SG CYS A 981 " pdb=" SG CYS A 991 " pdb=" CB CYS A 991 " ideal model delta sinusoidal sigma weight residual 93.00 139.96 -46.96 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA SER A1176 " pdb=" C SER A1176 " pdb=" N PRO A1177 " pdb=" CA PRO A1177 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN A 505 " pdb=" C ASN A 505 " pdb=" N TYR A 506 " pdb=" CA TYR A 506 " ideal model delta harmonic sigma weight residual 180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1046 0.082 - 0.164: 176 0.164 - 0.246: 17 0.246 - 0.329: 8 0.329 - 0.411: 3 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB VAL A 526 " pdb=" CA VAL A 526 " pdb=" CG1 VAL A 526 " pdb=" CG2 VAL A 526 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 686 " pdb=" CA ILE A 686 " pdb=" CG1 ILE A 686 " pdb=" CG2 ILE A 686 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE A 982 " pdb=" CA ILE A 982 " pdb=" CG1 ILE A 982 " pdb=" CG2 ILE A 982 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 1247 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 336 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C HIS A 336 " 0.068 2.00e-02 2.50e+03 pdb=" O HIS A 336 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 337 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 966 " 0.035 2.00e-02 2.50e+03 3.38e-02 1.43e+01 pdb=" CG ASN A 966 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 966 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 966 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.018 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE A 347 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " -0.001 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2664 2.86 - 3.37: 6039 3.37 - 3.88: 13927 3.88 - 4.39: 15143 4.39 - 4.90: 26946 Nonbonded interactions: 64719 Sorted by model distance: nonbonded pdb=" O LYS A 250 " pdb=" OG1 THR A 254 " model vdw 2.356 3.040 nonbonded pdb=" OG SER A1225 " pdb=" O GLY A1227 " model vdw 2.377 3.040 nonbonded pdb=" OG SER A 933 " pdb=" OG SER A 937 " model vdw 2.384 3.040 nonbonded pdb=" OE1 GLN A 352 " pdb=" NH2 ARG A 406 " model vdw 2.414 3.120 nonbonded pdb=" N SER A 862 " pdb=" O SER A 862 " model vdw 2.433 2.496 ... (remaining 64714 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.030 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:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.007 0.062 8493 Z= 0.336 Angle : 1.241 16.916 11572 Z= 0.668 Chirality : 0.066 0.411 1250 Planarity : 0.010 0.089 1506 Dihedral : 13.561 89.833 3190 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.41 % 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: -2.06 (0.24), residues: 1022 helix: -3.73 (0.32), residues: 73 sheet: -0.52 (0.24), residues: 438 loop : -1.74 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 882 TYR 0.036 0.003 TYR A 740 PHE 0.063 0.004 PHE A 347 TRP 0.056 0.003 TRP A 333 HIS 0.013 0.002 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 8482) covalent geometry : angle 1.23463 (11546) SS BOND : bond 0.00385 ( 7) SS BOND : angle 2.77125 ( 14) hydrogen bonds : bond 0.21333 ( 268) hydrogen bonds : angle 9.21658 ( 714) link_BETA1-4 : bond 0.00261 ( 1) link_BETA1-4 : angle 3.92897 ( 3) link_NAG-ASN : bond 0.01567 ( 3) link_NAG-ASN : angle 2.72395 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8040 (pt0) cc_final: 0.7826 (pt0) REVERT: A 265 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8087 (mtmt) REVERT: A 462 ARG cc_start: 0.7817 (ttt90) cc_final: 0.7103 (tmt-80) REVERT: A 507 THR cc_start: 0.7964 (m) cc_final: 0.7730 (p) REVERT: A 600 GLU cc_start: 0.8148 (pp20) cc_final: 0.7894 (pm20) REVERT: A 859 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7126 (mmp-170) REVERT: A 868 LEU cc_start: 0.8479 (tp) cc_final: 0.8261 (OUTLIER) REVERT: A 889 GLN cc_start: 0.8637 (mt0) cc_final: 0.8271 (mm-40) REVERT: A 935 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7406 (pm20) REVERT: A 978 LEU cc_start: 0.8266 (mt) cc_final: 0.8043 (mm) REVERT: A 1120 GLN cc_start: 0.7055 (mp10) cc_final: 0.6689 (mp10) REVERT: A 1150 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7978 (ttp80) REVERT: A 1199 MET cc_start: 0.8025 (ptm) cc_final: 0.7410 (mmm) REVERT: A 1239 PHE cc_start: 0.8163 (p90) cc_final: 0.7889 (p90) outliers start: 0 outliers final: 2 residues processed: 157 average time/residue: 0.5166 time to fit residues: 85.5397 Evaluate side-chains 98 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 501 GLN A 563 ASN A1124 GLN A1174 GLN A1264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105967 restraints weight = 10231.227| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.69 r_work: 0.3108 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8493 Z= 0.156 Angle : 0.623 6.699 11572 Z= 0.316 Chirality : 0.043 0.158 1250 Planarity : 0.006 0.049 1506 Dihedral : 5.420 27.762 1216 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.05 % Allowed : 8.67 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.25 (0.25), residues: 1022 helix: -0.95 (0.54), residues: 76 sheet: -0.39 (0.25), residues: 444 loop : -1.15 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 550 TYR 0.017 0.001 TYR A 740 PHE 0.018 0.002 PHE A 651 TRP 0.021 0.002 TRP A 333 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8482) covalent geometry : angle 0.61798 (11546) SS BOND : bond 0.00270 ( 7) SS BOND : angle 0.94232 ( 14) hydrogen bonds : bond 0.04014 ( 268) hydrogen bonds : angle 6.31851 ( 714) link_BETA1-4 : bond 0.01071 ( 1) link_BETA1-4 : angle 3.07642 ( 3) link_NAG-ASN : bond 0.00875 ( 3) link_NAG-ASN : angle 2.11169 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7745 (mtmt) REVERT: A 462 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7091 (tmt-80) REVERT: A 603 GLN cc_start: 0.8350 (mm110) cc_final: 0.8018 (mm110) REVERT: A 719 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7979 (mm-40) REVERT: A 882 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8142 (mmp80) REVERT: A 1150 ARG cc_start: 0.8226 (ttm110) cc_final: 0.8017 (ttp80) REVERT: A 1167 MET cc_start: 0.8154 (mtp) cc_final: 0.7541 (mtm) REVERT: A 1199 MET cc_start: 0.8042 (ptm) cc_final: 0.7748 (mmm) outliers start: 18 outliers final: 2 residues processed: 104 average time/residue: 0.4924 time to fit residues: 54.3251 Evaluate side-chains 81 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1090 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104943 restraints weight = 10186.892| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.72 r_work: 0.3091 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8493 Z= 0.124 Angle : 0.561 6.235 11572 Z= 0.279 Chirality : 0.042 0.159 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.780 25.784 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.94 % Allowed : 12.54 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.67 (0.26), residues: 1022 helix: 0.72 (0.64), residues: 72 sheet: -0.38 (0.24), residues: 459 loop : -0.56 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 492 TYR 0.013 0.001 TYR A 740 PHE 0.014 0.001 PHE A 651 TRP 0.018 0.001 TRP A 333 HIS 0.005 0.001 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8482) covalent geometry : angle 0.55670 (11546) SS BOND : bond 0.00191 ( 7) SS BOND : angle 0.68554 ( 14) hydrogen bonds : bond 0.03321 ( 268) hydrogen bonds : angle 5.66440 ( 714) link_BETA1-4 : bond 0.00739 ( 1) link_BETA1-4 : angle 2.06021 ( 3) link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 2.36253 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7647 (mtmt) REVERT: A 462 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7143 (ttt-90) REVERT: A 550 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8169 (tpp-160) REVERT: A 553 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (mmm) REVERT: A 565 MET cc_start: 0.8722 (tpp) cc_final: 0.8418 (tpp) REVERT: A 603 GLN cc_start: 0.8373 (mm110) cc_final: 0.8096 (mm110) REVERT: A 1150 ARG cc_start: 0.8247 (ttm110) cc_final: 0.8017 (ttp80) REVERT: A 1167 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: A 1243 LEU cc_start: 0.8754 (mp) cc_final: 0.8511 (mt) outliers start: 17 outliers final: 3 residues processed: 105 average time/residue: 0.4079 time to fit residues: 45.8575 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 278 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100875 restraints weight = 10396.281| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.69 r_work: 0.3092 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8493 Z= 0.146 Angle : 0.560 6.414 11572 Z= 0.276 Chirality : 0.042 0.143 1250 Planarity : 0.004 0.037 1506 Dihedral : 4.685 25.957 1214 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 13.45 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.42 (0.26), residues: 1022 helix: 1.25 (0.66), residues: 72 sheet: -0.31 (0.25), residues: 458 loop : -0.35 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.019 0.001 TYR A 567 PHE 0.013 0.001 PHE A 735 TRP 0.016 0.001 TRP A 623 HIS 0.007 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8482) covalent geometry : angle 0.55201 (11546) SS BOND : bond 0.00228 ( 7) SS BOND : angle 0.61619 ( 14) hydrogen bonds : bond 0.03055 ( 268) hydrogen bonds : angle 5.47511 ( 714) link_BETA1-4 : bond 0.00871 ( 1) link_BETA1-4 : angle 1.90430 ( 3) link_NAG-ASN : bond 0.00613 ( 3) link_NAG-ASN : angle 3.22645 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7617 (mtmt) REVERT: A 266 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: A 384 ASP cc_start: 0.8188 (t70) cc_final: 0.7977 (t0) REVERT: A 462 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7461 (ttt-90) REVERT: A 550 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8378 (tpp-160) REVERT: A 603 GLN cc_start: 0.8460 (mm110) cc_final: 0.8216 (mm110) REVERT: A 1150 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8164 (ttp80) REVERT: A 1167 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7732 (mtm) REVERT: A 1243 LEU cc_start: 0.8801 (mp) cc_final: 0.8595 (mt) outliers start: 18 outliers final: 5 residues processed: 94 average time/residue: 0.3940 time to fit residues: 39.6908 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 61.3233 > 50: distance: 27 - 107: 31.429 distance: 30 - 36: 6.909 distance: 36 - 37: 7.931 distance: 37 - 38: 3.996 distance: 37 - 40: 8.597 distance: 38 - 39: 13.614 distance: 38 - 44: 12.940 distance: 40 - 41: 9.398 distance: 41 - 42: 5.128 distance: 41 - 43: 16.877 distance: 44 - 45: 9.355 distance: 45 - 46: 7.156 distance: 45 - 48: 12.715 distance: 46 - 47: 9.484 distance: 46 - 52: 13.228 distance: 48 - 49: 15.270 distance: 49 - 50: 14.689 distance: 49 - 51: 22.187 distance: 52 - 53: 5.062 distance: 53 - 54: 27.351 distance: 53 - 56: 19.230 distance: 54 - 55: 16.555 distance: 54 - 59: 22.197 distance: 56 - 57: 14.097 distance: 56 - 58: 31.836 distance: 59 - 60: 7.458 distance: 60 - 61: 11.361 distance: 60 - 63: 9.023 distance: 61 - 62: 5.149 distance: 61 - 69: 5.135 distance: 63 - 64: 35.802 distance: 64 - 65: 16.051 distance: 64 - 66: 19.942 distance: 65 - 67: 7.144 distance: 67 - 68: 22.237 distance: 69 - 70: 5.474 distance: 70 - 71: 11.421 distance: 70 - 73: 14.406 distance: 71 - 72: 20.023 distance: 71 - 75: 16.408 distance: 73 - 74: 13.081 distance: 75 - 76: 10.330 distance: 76 - 77: 19.976 distance: 76 - 79: 19.927 distance: 77 - 78: 34.378 distance: 77 - 84: 5.163 distance: 79 - 80: 11.739 distance: 80 - 81: 24.332 distance: 81 - 82: 7.034 distance: 81 - 83: 10.973 distance: 85 - 86: 11.288 distance: 86 - 87: 5.693 distance: 86 - 98: 26.154 distance: 88 - 89: 13.258 distance: 89 - 90: 31.883 distance: 89 - 91: 15.769 distance: 90 - 92: 10.678 distance: 91 - 93: 36.400 distance: 91 - 94: 18.351 distance: 92 - 93: 22.752 distance: 93 - 95: 9.529 distance: 94 - 96: 17.462 distance: 95 - 97: 16.258 distance: 96 - 97: 25.611 distance: 99 - 100: 15.861 distance: 100 - 101: 14.732 distance: 100 - 102: 8.269 distance: 102 - 103: 18.716 distance: 103 - 104: 18.079 distance: 103 - 106: 21.656 distance: 104 - 105: 20.850 distance: 104 - 108: 39.928 distance: 106 - 107: 35.475 distance: 108 - 109: 46.398 distance: 108 - 114: 50.664 distance: 109 - 110: 22.512 distance: 109 - 112: 19.747 distance: 110 - 111: 19.719 distance: 110 - 115: 21.156 distance: 112 - 113: 37.574