Starting phenix.real_space_refine on Sat Aug 23 09:45:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.cif Found real_map, /net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6klc_0706/08_2025/6klc_0706.map" } resolution = 3.9 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= 0.012 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: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 72 5.16 5 C 7134 2.51 5 N 1866 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 11210 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11209 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 41, 'TRANS': 1394} Chain breaks: 18 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 343 Planarities with less than four sites: {'ARG:plan': 13, 'GLU:plan': 13, 'PHE:plan': 9, 'GLN:plan1': 4, 'TRP:plan': 2, 'TYR:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.24 Number of scatterers: 11210 At special positions: 0 Unit cell: (119.68, 112.88, 125.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 72 16.00 O 2137 8.00 N 1866 7.00 C 7134 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: 0.99 Conformation dependent library (CDL) restraints added in 534.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.603A pdb=" N ILE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.997A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 170 through 177 removed outlier: 4.282A pdb=" N SER A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 232 through 249 removed outlier: 3.884A pdb=" N LEU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.896A pdb=" N PHE A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.533A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 removed outlier: 4.241A pdb=" N MET A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.530A pdb=" N ARG A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 411 No H-bonds generated for 'chain 'A' and resid 410 through 411' Processing helix chain 'A' and resid 415 through 415 No H-bonds generated for 'chain 'A' and resid 415 through 415' Processing helix chain 'A' and resid 416 through 436 removed outlier: 3.560A pdb=" N ASN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.725A pdb=" N ARG A 581 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE A 583 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.564A pdb=" N GLN A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.791A pdb=" N LEU A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.555A pdb=" N LEU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 846 through 862 Processing helix chain 'A' and resid 870 through 886 removed outlier: 3.640A pdb=" N LEU A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 912 through 929 removed outlier: 3.563A pdb=" N GLU A 929 " --> pdb=" O ASP A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1098 removed outlier: 4.004A pdb=" N LEU A1098 " --> pdb=" O MET A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1159 Processing helix chain 'A' and resid 1167 through 1184 removed outlier: 3.608A pdb=" N MET A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 removed outlier: 3.532A pdb=" N PHE A1205 " --> pdb=" O CYS A1201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1238 removed outlier: 3.848A pdb=" N LEU A1229 " --> pdb=" O GLY A1225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1237 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1238 " --> pdb=" O MET A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1270 through 1282 removed outlier: 3.646A pdb=" N GLY A1282 " --> pdb=" O ASN A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 removed outlier: 3.515A pdb=" N THR A1344 " --> pdb=" O ASP A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.642A pdb=" N PHE A1354 " --> pdb=" O ASP A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1408 removed outlier: 4.173A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1432 Processing helix chain 'A' and resid 1435 through 1452 removed outlier: 3.975A pdb=" N CYS A1439 " --> pdb=" O PRO A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1506 removed outlier: 3.593A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1518 removed outlier: 4.395A pdb=" N PHE A1515 " --> pdb=" O LEU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1580 through 1590 removed outlier: 4.232A pdb=" N LYS A1584 " --> pdb=" O PRO A1580 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A1590 " --> pdb=" O ILE A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 removed outlier: 3.670A pdb=" N GLY A1618 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O ILE A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1649 removed outlier: 3.773A pdb=" N ILE A1644 " --> pdb=" O TYR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1742 through 1752 Processing helix chain 'A' and resid 1781 through 1788 Processing helix chain 'A' and resid 1797 through 1802 removed outlier: 3.807A pdb=" N VAL A1802 " --> pdb=" O VAL A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1820 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.003A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 100 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 542 removed outlier: 3.557A pdb=" N PHE A 541 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1121 through 1126 removed outlier: 3.548A pdb=" N ARG A1133 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1326 through 1330 removed outlier: 3.894A pdb=" N GLY A1379 " --> pdb=" O SER A1188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1241 through 1242 Processing sheet with id=AA6, first strand: chain 'A' and resid 1382 through 1385 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AA8, first strand: chain 'A' and resid 1631 through 1632 600 hydrogen bonds defined for protein. 1752 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: 1.61 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 1968 1.45 - 1.57: 6361 1.57 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 11395 Sorted by residual: bond pdb=" N ASP A1334 " pdb=" CA ASP A1334 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.89e+00 bond pdb=" C VAL A1434 " pdb=" O VAL A1434 " ideal model delta sigma weight residual 1.240 1.213 0.027 1.26e-02 6.30e+03 4.48e+00 bond pdb=" N TYR A1452 " pdb=" CA TYR A1452 " ideal model delta sigma weight residual 1.458 1.430 0.027 1.33e-02 5.65e+03 4.12e+00 bond pdb=" CA ILE A 152 " pdb=" CB ILE A 152 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" C TYR A1455 " pdb=" O TYR A1455 " ideal model delta sigma weight residual 1.246 1.231 0.015 9.20e-03 1.18e+04 2.72e+00 ... (remaining 11390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14610 1.41 - 2.82: 659 2.82 - 4.22: 99 4.22 - 5.63: 31 5.63 - 7.04: 11 Bond angle restraints: 15410 Sorted by residual: angle pdb=" C TYR A1455 " pdb=" N PRO A1456 " pdb=" CA PRO A1456 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.86e+01 angle pdb=" N VAL A 690 " pdb=" CA VAL A 690 " pdb=" C VAL A 690 " ideal model delta sigma weight residual 113.47 108.15 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" N VAL A1436 " pdb=" CA VAL A1436 " pdb=" C VAL A1436 " ideal model delta sigma weight residual 110.36 115.66 -5.30 1.05e+00 9.07e-01 2.54e+01 angle pdb=" N THR A1116 " pdb=" CA THR A1116 " pdb=" C THR A1116 " ideal model delta sigma weight residual 114.04 109.13 4.91 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N TYR A1665 " pdb=" CA TYR A1665 " pdb=" C TYR A1665 " ideal model delta sigma weight residual 108.13 114.23 -6.10 1.72e+00 3.38e-01 1.26e+01 ... (remaining 15405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6309 17.59 - 35.19: 506 35.19 - 52.78: 85 52.78 - 70.37: 13 70.37 - 87.96: 6 Dihedral angle restraints: 6919 sinusoidal: 2698 harmonic: 4221 Sorted by residual: dihedral pdb=" CA ARG A 336 " pdb=" C ARG A 336 " pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N MET A 707 " pdb=" CA MET A 707 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1653 0.071 - 0.143: 145 0.143 - 0.214: 10 0.214 - 0.286: 1 0.286 - 0.357: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA HIS A 443 " pdb=" N HIS A 443 " pdb=" C HIS A 443 " pdb=" CB HIS A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA HIS A1437 " pdb=" N HIS A1437 " pdb=" C HIS A1437 " pdb=" CB HIS A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN A1432 " pdb=" N ASN A1432 " pdb=" C ASN A1432 " pdb=" CB ASN A1432 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 1807 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1431 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ALA A1431 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A1431 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN A1432 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1333 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A1333 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A1333 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A1334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 153 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.029 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1013 2.74 - 3.28: 11920 3.28 - 3.82: 17702 3.82 - 4.36: 20024 4.36 - 4.90: 34375 Nonbonded interactions: 85034 Sorted by model distance: nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU A 731 " pdb=" OG1 THR A1271 " model vdw 2.217 3.040 nonbonded pdb=" O SER A 440 " pdb=" OG SER A 440 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASP A 89 " pdb=" N CYS A 103 " model vdw 2.281 3.120 nonbonded pdb=" NH1 ARG A 643 " pdb=" OH TYR A 706 " model vdw 2.282 3.120 ... (remaining 85029 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.290 Find NCS groups from input model: 0.050 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11395 Z= 0.168 Angle : 0.700 7.040 15410 Z= 0.426 Chirality : 0.043 0.357 1810 Planarity : 0.003 0.053 1949 Dihedral : 13.241 87.964 4165 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.30 % Favored : 90.49 % Rotamer: Outliers : 0.64 % Allowed : 5.06 % Favored : 94.30 % 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: -3.27 (0.19), residues: 1398 helix: -1.02 (0.16), residues: 789 sheet: -1.64 (0.49), residues: 108 loop : -4.21 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.014 0.001 TYR A 706 PHE 0.011 0.001 PHE A 104 TRP 0.007 0.001 TRP A1704 HIS 0.005 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00300 (11395) covalent geometry : angle 0.70029 (15410) hydrogen bonds : bond 0.12718 ( 600) hydrogen bonds : angle 6.69663 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 359 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.5901 (ttm) cc_final: 0.5571 (ttm) REVERT: A 113 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 114 GLN cc_start: 0.7941 (tp40) cc_final: 0.7684 (tt0) REVERT: A 115 LYS cc_start: 0.8041 (tptt) cc_final: 0.7423 (tptt) REVERT: A 118 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6421 (tm-30) REVERT: A 240 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 241 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 325 TRP cc_start: 0.7701 (m100) cc_final: 0.7179 (m100) REVERT: A 407 MET cc_start: 0.8844 (mmp) cc_final: 0.8114 (mmt) REVERT: A 448 MET cc_start: 0.7376 (tmm) cc_final: 0.7106 (tmm) REVERT: A 660 ASP cc_start: 0.7612 (t0) cc_final: 0.7253 (t0) REVERT: A 727 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 856 LEU cc_start: 0.9525 (tp) cc_final: 0.8910 (tp) REVERT: A 860 PHE cc_start: 0.7793 (m-80) cc_final: 0.7425 (m-80) REVERT: A 925 ASP cc_start: 0.8953 (t0) cc_final: 0.8688 (t0) REVERT: A 926 GLN cc_start: 0.9020 (pp30) cc_final: 0.8733 (pp30) REVERT: A 1094 MET cc_start: 0.3657 (pmm) cc_final: 0.3317 (pmm) REVERT: A 1151 ASP cc_start: 0.8649 (p0) cc_final: 0.8420 (p0) REVERT: A 1160 LEU cc_start: 0.9142 (mt) cc_final: 0.8917 (mp) REVERT: A 1242 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 1253 LYS cc_start: 0.8353 (tptp) cc_final: 0.8042 (mmtt) REVERT: A 1341 GLN cc_start: 0.8304 (pp30) cc_final: 0.7747 (pp30) REVERT: A 1364 MET cc_start: 0.7935 (mmm) cc_final: 0.7592 (tpp) REVERT: A 1436 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 1479 ARG cc_start: 0.7935 (mtt90) cc_final: 0.6928 (mtm180) REVERT: A 1485 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 1551 ASN cc_start: 0.7951 (t0) cc_final: 0.7448 (t0) REVERT: A 1629 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7901 (mmtp) REVERT: A 1797 LEU cc_start: 0.6333 (mt) cc_final: 0.5891 (mm) outliers start: 8 outliers final: 5 residues processed: 365 average time/residue: 0.1189 time to fit residues: 60.1040 Evaluate side-chains 252 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 67.4705 > 50: distance: 58 - 75: 20.620 distance: 62 - 86: 23.073 distance: 66 - 93: 27.416 distance: 71 - 75: 21.707 distance: 75 - 76: 25.818 distance: 76 - 77: 25.384 distance: 76 - 79: 15.747 distance: 77 - 78: 11.339 distance: 77 - 86: 23.197 distance: 79 - 80: 31.380 distance: 80 - 81: 14.405 distance: 81 - 82: 13.619 distance: 82 - 83: 11.356 distance: 83 - 84: 10.067 distance: 83 - 85: 13.289 distance: 86 - 87: 26.460 distance: 87 - 88: 39.427 distance: 87 - 90: 52.866 distance: 88 - 89: 52.768 distance: 88 - 93: 25.834 distance: 90 - 91: 39.384 distance: 90 - 92: 54.561 distance: 93 - 94: 16.469 distance: 94 - 95: 12.642 distance: 94 - 97: 26.175 distance: 95 - 96: 22.419 distance: 95 - 101: 20.036 distance: 97 - 98: 44.724 distance: 98 - 99: 41.874 distance: 98 - 100: 46.796 distance: 101 - 102: 41.782 distance: 102 - 103: 32.039 distance: 103 - 104: 10.523 distance: 103 - 105: 18.821 distance: 105 - 106: 18.271 distance: 106 - 107: 12.155 distance: 106 - 109: 10.172 distance: 107 - 108: 5.210 distance: 107 - 111: 31.321 distance: 109 - 110: 38.788 distance: 111 - 112: 14.877 distance: 112 - 113: 14.139 distance: 112 - 115: 23.189 distance: 113 - 114: 22.729 distance: 113 - 120: 17.546 distance: 115 - 116: 24.761 distance: 116 - 117: 21.480 distance: 117 - 118: 15.407 distance: 118 - 119: 5.825 distance: 120 - 121: 24.404 distance: 121 - 122: 37.048 distance: 121 - 124: 27.919 distance: 122 - 123: 27.772 distance: 122 - 126: 35.303 distance: 124 - 125: 19.441 distance: 126 - 127: 23.086 distance: 126 - 177: 16.997 distance: 127 - 128: 16.163 distance: 127 - 130: 8.776 distance: 128 - 129: 12.198 distance: 128 - 133: 12.381 distance: 129 - 174: 29.607 distance: 130 - 131: 19.162 distance: 130 - 132: 28.736 distance: 133 - 134: 10.231 distance: 134 - 135: 10.716 distance: 134 - 137: 6.269 distance: 135 - 136: 26.471 distance: 135 - 144: 22.390 distance: 137 - 138: 13.205 distance: 138 - 139: 33.240 distance: 139 - 140: 7.168 distance: 140 - 141: 17.123 distance: 141 - 142: 14.121 distance: 141 - 143: 8.066 distance: 144 - 145: 21.777 distance: 145 - 146: 22.362 distance: 146 - 147: 14.338 distance: 146 - 148: 10.648