Starting phenix.real_space_refine on Fri Aug 22 21:01:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ien_35387/08_2025/8ien_35387.map" } resolution = 3.25 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= 0.003 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 4959 2.51 5 N 1320 2.21 5 O 1340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 7678 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7644 Classifications: {'peptide': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 65, 'TRANS': 922} Chain breaks: 6 Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.09, per 1000 atoms: 0.27 Number of scatterers: 7678 At special positions: 0 Unit cell: (86.505, 112.785, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1340 8.00 N 1320 7.00 C 4959 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 432.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 48.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'P' and resid 50 through 59 Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 69 through 77 removed outlier: 3.828A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 201 Processing helix chain 'P' and resid 208 through 217 removed outlier: 3.652A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 236 Processing helix chain 'P' and resid 238 through 254 Processing helix chain 'P' and resid 256 through 290 Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 403 through 413 removed outlier: 4.003A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS P 413 " --> pdb=" O SER P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 451 removed outlier: 3.719A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG P 451 " --> pdb=" O LEU P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 469 removed outlier: 3.582A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL P 469 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 492 removed outlier: 4.347A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR P 481 " --> pdb=" O MET P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 504 removed outlier: 4.416A pdb=" N ASN P 502 " --> pdb=" O PRO P 498 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 503 " --> pdb=" O LEU P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 558 Processing helix chain 'P' and resid 571 through 581 Processing helix chain 'P' and resid 656 through 664 removed outlier: 3.583A pdb=" N VAL P 660 " --> pdb=" O SER P 656 " (cutoff:3.500A) Processing helix chain 'P' and resid 673 through 683 removed outlier: 3.614A pdb=" N LEU P 677 " --> pdb=" O PHE P 673 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 742 removed outlier: 3.754A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 765 removed outlier: 3.520A pdb=" N ALA P 757 " --> pdb=" O ASN P 753 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 835 Processing helix chain 'P' and resid 840 through 847 Processing helix chain 'P' and resid 855 through 868 Processing helix chain 'P' and resid 882 through 889 Processing helix chain 'P' and resid 914 through 955 removed outlier: 4.249A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 Processing helix chain 'P' and resid 970 through 978 Processing helix chain 'P' and resid 998 through 1026 removed outlier: 3.750A pdb=" N LEU P1017 " --> pdb=" O THR P1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P1018 " --> pdb=" O GLY P1014 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P1019 " --> pdb=" O VAL P1015 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR P1020 " --> pdb=" O GLN P1016 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1037 through 1041 removed outlier: 3.651A pdb=" N ASN P1041 " --> pdb=" O ALA P1038 " (cutoff:3.500A) Processing helix chain 'P' and resid 1044 through 1065 removed outlier: 3.776A pdb=" N THR P1048 " --> pdb=" O ASN P1044 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1098 Processing helix chain 'P' and resid 1113 through 1139 Processing helix chain 'P' and resid 1141 through 1146 Processing helix chain 'P' and resid 1156 through 1169 Processing sheet with id=AA1, first strand: chain 'P' and resid 40 through 41 removed outlier: 4.136A pdb=" N CYS P 41 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 90 " --> pdb=" O CYS P 41 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE P 103 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU P 167 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 303 through 308 removed outlier: 3.843A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS P 296 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N CYS P 317 " --> pdb=" O CYS P 298 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR P 396 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP P 330 " --> pdb=" O THR P 396 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA P 331 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 374 " --> pdb=" O ALA P 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 351 through 354 removed outlier: 3.770A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 493 through 495 removed outlier: 5.895A pdb=" N GLY P 892 " --> pdb=" O PHE P 906 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER P 908 " --> pdb=" O GLY P 892 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER P 894 " --> pdb=" O SER P 908 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL P 873 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE P 893 " --> pdb=" O VAL P 873 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU P 509 " --> pdb=" O GLY P 874 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N CYS P 876 " --> pdb=" O LEU P 509 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS P 511 " --> pdb=" O CYS P 876 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 849 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 823 " --> pdb=" O GLY P 848 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS P 772 " --> pdb=" O ALA P 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 788 " --> pdb=" O LEU P 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 624 through 627 removed outlier: 4.350A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA P 689 " --> pdb=" O GLY P 655 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P 720 " --> pdb=" O LEU P 690 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER P 692 " --> pdb=" O LEU P 718 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU P 718 " --> pdb=" O SER P 692 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1071 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: 1.32 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2449 1.35 - 1.46: 1687 1.46 - 1.58: 3623 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7842 Sorted by residual: bond pdb=" C11 SPM P1204 " pdb=" C12 SPM P1204 " ideal model delta sigma weight residual 1.527 1.395 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C12 SPM P1204 " pdb=" C13 SPM P1204 " ideal model delta sigma weight residual 1.527 1.407 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.26: 10663 14.26 - 28.52: 4 28.52 - 42.78: 0 42.78 - 57.04: 0 57.04 - 71.30: 2 Bond angle restraints: 10669 Sorted by residual: angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F2 ALF P1202 " ideal model delta sigma weight residual 108.68 179.98 -71.30 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 109.63 180.00 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.69 90.01 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.59 90.01 19.58 3.00e+00 1.11e-01 4.26e+01 ... (remaining 10664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4247 17.68 - 35.35: 401 35.35 - 53.03: 71 53.03 - 70.70: 16 70.70 - 88.38: 5 Dihedral angle restraints: 4740 sinusoidal: 1880 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ASP P 189 " pdb=" CB ASP P 189 " pdb=" CG ASP P 189 " pdb=" OD1 ASP P 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU P 650 " pdb=" CG GLU P 650 " pdb=" CD GLU P 650 " pdb=" OE1 GLU P 650 " ideal model delta sinusoidal sigma weight residual 0.00 88.38 -88.38 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 996 0.044 - 0.088: 197 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA SER P 425 " pdb=" N SER P 425 " pdb=" C SER P 425 " pdb=" CB SER P 425 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS P 424 " pdb=" N HIS P 424 " pdb=" C HIS P 424 " pdb=" CB HIS P 424 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PRO P 618 " pdb=" N PRO P 618 " pdb=" C PRO P 618 " pdb=" CB PRO P 618 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1263 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO P 618 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO P 619 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 426 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET P 426 " -0.030 2.00e-02 2.50e+03 pdb=" O MET P 426 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS P 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P1042 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO P1043 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO P1043 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1043 " -0.019 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 215 2.71 - 3.26: 7394 3.26 - 3.81: 11972 3.81 - 4.35: 14110 4.35 - 4.90: 24051 Nonbonded interactions: 57742 Sorted by model distance: nonbonded pdb="MG MG P1201 " pdb=" F1 ALF P1202 " model vdw 2.168 2.120 nonbonded pdb=" CG2 VAL P 467 " pdb=" C12 SPM P1204 " model vdw 2.241 3.860 nonbonded pdb=" OD2 ASP P 513 " pdb="MG MG P1201 " model vdw 2.252 2.170 nonbonded pdb=" O THR P 515 " pdb="MG MG P1201 " model vdw 2.280 2.170 nonbonded pdb=" CZ3 TRP P 251 " pdb=" C9 SPM P1204 " model vdw 2.282 3.740 ... (remaining 57737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.910 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.220 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0170 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 : 0.009 0.737 7844 Z= 0.880 Angle : 1.211 71.295 10669 Z= 0.486 Chirality : 0.040 0.220 1266 Planarity : 0.004 0.050 1339 Dihedral : 14.043 88.379 2894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -2.18 (0.25), residues: 977 helix: -0.46 (0.23), residues: 450 sheet: -1.34 (0.62), residues: 61 loop : -2.50 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P1148 TYR 0.015 0.001 TYR P 256 PHE 0.015 0.001 PHE P1128 TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7842) covalent geometry : angle 1.21135 (10669) hydrogen bonds : bond 0.17266 ( 362) hydrogen bonds : angle 5.73938 ( 1071) Misc. bond : bond 0.53561 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2583 (pt) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1443 (tpp) REVERT: P 577 MET cc_start: 0.1892 (mtp) cc_final: 0.0826 (tmm) REVERT: P 637 MET cc_start: 0.1190 (tmm) cc_final: 0.0944 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.0854 time to fit residues: 10.4711 Evaluate side-chains 54 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 101 GLN P 198 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 281 GLN P 559 HIS ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P1127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.253319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.223555 restraints weight = 11592.833| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 2.59 r_work: 0.4470 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0806 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7844 Z= 0.149 Angle : 0.924 32.847 10669 Z= 0.381 Chirality : 0.042 0.144 1266 Planarity : 0.005 0.045 1339 Dihedral : 5.782 57.580 1095 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.24 % Allowed : 9.70 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.19 (0.26), residues: 977 helix: 0.39 (0.24), residues: 451 sheet: -0.50 (0.61), residues: 76 loop : -2.14 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 279 TYR 0.025 0.002 TYR P 483 PHE 0.011 0.002 PHE P1128 TRP 0.018 0.001 TRP P 251 HIS 0.004 0.001 HIS P 424 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7842) covalent geometry : angle 0.92424 (10669) hydrogen bonds : bond 0.03862 ( 362) hydrogen bonds : angle 4.36303 ( 1071) Misc. bond : bond 0.00536 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3162 (mt) cc_final: 0.2755 (pt) REVERT: P 288 MET cc_start: -0.0401 (ptt) cc_final: -0.1166 (tpt) REVERT: P 477 MET cc_start: 0.1560 (tpp) cc_final: 0.1283 (mmm) REVERT: P 526 MET cc_start: -0.0751 (pmm) cc_final: -0.2151 (tmm) REVERT: P 573 MET cc_start: 0.3629 (ptt) cc_final: 0.2461 (mmm) REVERT: P 577 MET cc_start: 0.2677 (mtp) cc_final: 0.0963 (tmm) REVERT: P 637 MET cc_start: -0.0125 (tmm) cc_final: -0.0421 (mtp) REVERT: P 978 MET cc_start: 0.2636 (mtt) cc_final: 0.1388 (mmm) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.0636 time to fit residues: 6.1029 Evaluate side-chains 52 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 429 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 chunk 27 optimal weight: 0.0000 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 81 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P 962 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.255447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.225631 restraints weight = 11691.865| |-----------------------------------------------------------------------------| r_work (start): 0.4580 rms_B_bonded: 2.66 r_work: 0.4480 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0915 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7844 Z= 0.115 Angle : 0.871 29.581 10669 Z= 0.351 Chirality : 0.040 0.148 1266 Planarity : 0.004 0.044 1339 Dihedral : 5.325 58.212 1095 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.95 % Allowed : 12.07 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.70 (0.27), residues: 977 helix: 0.94 (0.25), residues: 448 sheet: -0.35 (0.58), residues: 76 loop : -2.01 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 279 TYR 0.025 0.001 TYR P 483 PHE 0.009 0.001 PHE P1128 TRP 0.006 0.001 TRP P 643 HIS 0.007 0.001 HIS P 84 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7842) covalent geometry : angle 0.87055 (10669) hydrogen bonds : bond 0.03042 ( 362) hydrogen bonds : angle 4.07206 ( 1071) Misc. bond : bond 0.00236 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.3197 (mt) cc_final: 0.2796 (pt) REVERT: P 288 MET cc_start: -0.0289 (ptt) cc_final: -0.1113 (tpp) REVERT: P 526 MET cc_start: -0.0214 (pmm) cc_final: -0.2522 (tmm) REVERT: P 577 MET cc_start: 0.2754 (mtp) cc_final: 0.0847 (tmm) REVERT: P 978 MET cc_start: 0.2521 (mtt) cc_final: 0.1711 (mmm) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.0584 time to fit residues: 5.6972 Evaluate side-chains 52 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 275 LEU Chi-restraints excluded: chain P residue 724 MET 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: 70.3051 > 50: distance: 20 - 43: 25.800 distance: 38 - 43: 26.196 distance: 43 - 44: 14.560 distance: 44 - 45: 32.232 distance: 44 - 47: 32.029 distance: 45 - 46: 19.940 distance: 45 - 52: 54.323 distance: 47 - 48: 21.119 distance: 48 - 49: 3.646 distance: 49 - 50: 26.725 distance: 50 - 51: 13.589 distance: 52 - 53: 30.036 distance: 53 - 54: 35.589 distance: 53 - 56: 34.078 distance: 54 - 55: 35.143 distance: 54 - 60: 46.003 distance: 56 - 57: 4.849 distance: 57 - 58: 12.482 distance: 57 - 59: 38.980 distance: 60 - 61: 14.144 distance: 61 - 62: 32.202 distance: 61 - 64: 20.875 distance: 62 - 63: 20.531 distance: 62 - 66: 38.909 distance: 64 - 65: 19.177 distance: 66 - 67: 16.460 distance: 67 - 68: 29.475 distance: 67 - 70: 39.798 distance: 68 - 69: 24.694 distance: 68 - 74: 16.533 distance: 70 - 71: 7.345 distance: 71 - 72: 31.352 distance: 72 - 73: 22.932 distance: 74 - 75: 21.863 distance: 75 - 76: 39.116 distance: 75 - 78: 18.781 distance: 76 - 77: 23.889 distance: 76 - 85: 34.108 distance: 78 - 79: 38.652 distance: 79 - 80: 8.564 distance: 80 - 81: 17.894 distance: 81 - 82: 8.918 distance: 82 - 83: 10.772 distance: 82 - 84: 11.254 distance: 85 - 86: 19.367 distance: 85 - 178: 27.254 distance: 86 - 87: 31.115 distance: 86 - 89: 22.312 distance: 87 - 88: 42.196 distance: 87 - 92: 49.609 distance: 88 - 175: 34.082 distance: 89 - 90: 31.418 distance: 89 - 91: 13.109 distance: 92 - 93: 19.908 distance: 93 - 94: 10.325 distance: 93 - 96: 38.326 distance: 95 - 215: 33.761 distance: 96 - 97: 37.535 distance: 98 - 99: 27.033 distance: 98 - 155: 35.078 distance: 99 - 100: 12.487 distance: 99 - 102: 5.132 distance: 100 - 101: 15.084 distance: 101 - 152: 28.477 distance: 102 - 103: 8.306 distance: 102 - 104: 26.515 distance: 105 - 106: 5.255 distance: 105 - 205: 37.052 distance: 106 - 107: 20.882 distance: 106 - 109: 31.273 distance: 107 - 108: 33.655 distance: 107 - 111: 12.276 distance: 109 - 110: 36.041 distance: 111 - 112: 12.426 distance: 111 - 138: 26.718 distance: 112 - 113: 47.440 distance: 112 - 115: 27.322 distance: 113 - 114: 9.713 distance: 113 - 122: 30.656 distance: 115 - 116: 25.206 distance: 116 - 117: 41.971 distance: 117 - 118: 8.849 distance: 118 - 119: 14.648 distance: 119 - 120: 36.567 distance: 119 - 121: 29.325