Starting phenix.real_space_refine on Sun Jan 19 19:02:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.map" model { file = "/net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/01_2025/7yna_33956.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 63 5.49 5 S 57 5.16 5 C 8468 2.51 5 N 2454 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 527 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 21} Time building chain proxies: 10.64, per 1000 atoms: 0.77 Number of scatterers: 13784 At special positions: 0 Unit cell: (92.02, 171.2, 132.68, 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) S 57 16.00 P 63 15.00 O 2742 8.00 N 2454 7.00 C 8468 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: 3.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 22.2% alpha, 15.3% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.510A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.037A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.945A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.080A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.613A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.562A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.651A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.650A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.986A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 4.178A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1108 " --> pdb=" O ASP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1246 removed outlier: 3.980A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.132A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.975A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 removed outlier: 3.646A pdb=" N GLN A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.032A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1569 " --> pdb=" O LYS A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1569' Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.569A pdb=" N THR A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.709A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.630A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.742A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.743A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.518A pdb=" N LEU A 728 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.594A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 993 removed outlier: 4.035A pdb=" N VAL A1275 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1001 through 1011 removed outlier: 8.390A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 19.405A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.370A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1044 through 1047 Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.670A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AC2, first strand: chain 'A' and resid 1385 through 1387 307 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 4.08 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: 3596 1.33 - 1.45: 2944 1.45 - 1.57: 7491 1.57 - 1.69: 124 1.69 - 1.81: 82 Bond restraints: 14237 Sorted by residual: bond pdb=" C CYS A1560 " pdb=" N TYR A1561 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.42e+00 bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" N CYS A 706 " pdb=" CA CYS A 706 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19113 2.23 - 4.45: 342 4.45 - 6.68: 25 6.68 - 8.91: 3 8.91 - 11.13: 1 Bond angle restraints: 19484 Sorted by residual: angle pdb=" N SER A1080 " pdb=" CA SER A1080 " pdb=" C SER A1080 " ideal model delta sigma weight residual 108.34 113.35 -5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N LYS A1586 " pdb=" CA LYS A1586 " pdb=" C LYS A1586 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" CA CYS A 708 " pdb=" C CYS A 708 " pdb=" O CYS A 708 " ideal model delta sigma weight residual 121.55 118.02 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" N GLN A 884 " pdb=" CA GLN A 884 " pdb=" C GLN A 884 " ideal model delta sigma weight residual 110.80 103.99 6.81 2.13e+00 2.20e-01 1.02e+01 angle pdb=" C SER A1403 " pdb=" N ASP A1404 " pdb=" CA ASP A1404 " ideal model delta sigma weight residual 121.54 115.60 5.94 1.91e+00 2.74e-01 9.69e+00 ... (remaining 19479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 8376 34.14 - 68.28: 289 68.28 - 102.42: 35 102.42 - 136.56: 2 136.56 - 170.70: 1 Dihedral angle restraints: 8703 sinusoidal: 4272 harmonic: 4431 Sorted by residual: dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 173 " pdb=" C LEU A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U B -14 " pdb=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sinusoidal sigma weight residual -110.00 60.70 -170.70 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1524 0.048 - 0.097: 440 0.097 - 0.145: 103 0.145 - 0.193: 13 0.193 - 0.241: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA CYS A1342 " pdb=" N CYS A1342 " pdb=" C CYS A1342 " pdb=" CB CYS A1342 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2081 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 864 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.037 2.00e-02 2.50e+03 1.69e-02 8.56e+00 pdb=" N9 G B 9 " 0.043 2.00e-02 2.50e+03 pdb=" C8 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1311 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C PRO A1311 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A1311 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A1312 " -0.015 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 609 2.69 - 3.25: 13133 3.25 - 3.80: 20329 3.80 - 4.35: 25821 4.35 - 4.90: 44074 Nonbonded interactions: 103966 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 445 " pdb=" OP1 A B -2 " model vdw 2.186 3.040 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.229 3.120 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.241 3.120 nonbonded pdb=" NH1 ARG A 974 " pdb=" O ASP A1298 " model vdw 2.241 3.120 ... (remaining 103961 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 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: 3.540 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 0.064 14237 Z= 0.429 Angle : 0.729 11.132 19484 Z= 0.406 Chirality : 0.048 0.241 2084 Planarity : 0.005 0.079 2315 Dihedral : 16.960 170.704 5845 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.06 % Favored : 83.81 % Rotamer: Outliers : 0.60 % Allowed : 7.22 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.17), residues: 1526 helix: -1.14 (0.28), residues: 300 sheet: -3.22 (0.26), residues: 281 loop : -4.07 (0.15), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1600 HIS 0.005 0.002 HIS A1473 PHE 0.015 0.002 PHE A 528 TYR 0.021 0.002 TYR A 863 ARG 0.005 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.569 Fit side-chains REVERT: A 311 ASP cc_start: 0.8125 (t0) cc_final: 0.7676 (t70) REVERT: A 1065 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7252 (ttm170) REVERT: A 1211 MET cc_start: 0.7960 (tmm) cc_final: 0.7123 (tmm) REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7339 (mttm) REVERT: A 1342 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (p) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.3569 time to fit residues: 37.2889 Evaluate side-chains 48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1342 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 306 HIS A 456 GLN A 586 ASN A1095 HIS A1136 ASN A1207 ASN A1417 HIS A1419 HIS A1452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061922 restraints weight = 36282.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.063906 restraints weight = 19838.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.065179 restraints weight = 13986.925| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14237 Z= 0.167 Angle : 0.606 12.166 19484 Z= 0.315 Chirality : 0.043 0.209 2084 Planarity : 0.005 0.063 2315 Dihedral : 16.262 164.829 2639 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.37 % Allowed : 10.04 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1526 helix: 0.28 (0.31), residues: 311 sheet: -2.47 (0.28), residues: 275 loop : -3.72 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.011 0.001 PHE A 15 TYR 0.011 0.001 TYR A1081 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.439 Fit side-chains REVERT: A 305 ASP cc_start: 0.7358 (t0) cc_final: 0.6800 (t0) REVERT: A 410 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7725 (pp) REVERT: A 585 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7842 (tp30) REVERT: A 989 ASP cc_start: 0.8166 (t70) cc_final: 0.7938 (t0) REVERT: A 1065 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7198 (ttm170) REVERT: A 1211 MET cc_start: 0.7932 (tmm) cc_final: 0.7198 (tmm) REVERT: A 1270 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7307 (mttm) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.3173 time to fit residues: 32.9200 Evaluate side-chains 58 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5822 > 50: distance: 45 - 129: 13.025 distance: 48 - 126: 7.850 distance: 85 - 87: 6.211 distance: 87 - 88: 4.212 distance: 88 - 89: 4.913 distance: 88 - 91: 3.862 distance: 89 - 96: 4.626 distance: 91 - 92: 5.304 distance: 92 - 93: 6.219 distance: 93 - 94: 4.744 distance: 93 - 95: 3.696 distance: 97 - 98: 3.673 distance: 97 - 100: 8.540 distance: 98 - 105: 5.742 distance: 100 - 101: 7.578 distance: 101 - 102: 4.612 distance: 102 - 104: 3.047 distance: 105 - 106: 5.866 distance: 106 - 107: 16.129 distance: 106 - 109: 13.121 distance: 107 - 108: 12.099 distance: 107 - 110: 11.676 distance: 110 - 111: 12.701 distance: 111 - 112: 13.547 distance: 111 - 114: 18.786 distance: 112 - 113: 11.458 distance: 112 - 119: 8.062 distance: 114 - 115: 12.875 distance: 115 - 116: 7.277 distance: 116 - 117: 13.360 distance: 117 - 118: 9.574 distance: 119 - 120: 22.492 distance: 119 - 125: 15.289 distance: 120 - 121: 13.277 distance: 120 - 123: 25.287 distance: 121 - 122: 20.348 distance: 121 - 126: 20.654 distance: 123 - 124: 18.371 distance: 124 - 125: 18.343 distance: 126 - 127: 6.620 distance: 127 - 128: 6.515 distance: 127 - 130: 6.138 distance: 128 - 129: 3.928 distance: 128 - 133: 8.720 distance: 130 - 131: 19.262 distance: 130 - 132: 21.786 distance: 133 - 134: 14.316 distance: 134 - 135: 5.003 distance: 134 - 137: 14.294 distance: 135 - 136: 5.728 distance: 135 - 139: 7.240 distance: 137 - 138: 7.699 distance: 139 - 140: 9.217 distance: 140 - 141: 5.827 distance: 140 - 143: 11.109 distance: 141 - 142: 11.455 distance: 141 - 144: 16.021 distance: 144 - 145: 4.871 distance: 144 - 197: 6.618 distance: 145 - 146: 7.111 distance: 145 - 148: 5.944 distance: 146 - 147: 16.494 distance: 146 - 156: 13.968 distance: 148 - 149: 4.440 distance: 149 - 150: 13.300 distance: 149 - 151: 4.430 distance: 150 - 152: 4.612 distance: 151 - 153: 5.325 distance: 152 - 154: 5.302 distance: 153 - 154: 4.687 distance: 154 - 155: 5.390 distance: 156 - 157: 5.393 distance: 157 - 158: 11.946 distance: 157 - 160: 4.415 distance: 158 - 159: 13.290 distance: 158 - 165: 11.819 distance: 160 - 161: 16.093 distance: 161 - 162: 13.250 distance: 162 - 163: 8.997 distance: 163 - 164: 8.295