Starting phenix.real_space_refine on Wed Mar 12 07:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.map" model { file = "/net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n76_24221/03_2025/7n76_24221.cif" } resolution = 2.9 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4748 2.51 5 N 1280 2.21 5 O 1327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7396 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963} Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 650 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 549 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 6, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 347 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.84, per 1000 atoms: 0.65 Number of scatterers: 7399 At special positions: 0 Unit cell: (90.214, 102.802, 130.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1327 8.00 N 1280 7.00 C 4748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 52.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.194A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.508A pdb=" N MET A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 284 removed outlier: 3.532A pdb=" N SER A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.843A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.766A pdb=" N ASN A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.011A pdb=" N ARG A 540 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 667 through 678 removed outlier: 3.524A pdb=" N ALA A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 removed outlier: 3.704A pdb=" N GLN A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.581A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.535A pdb=" N THR A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 974 removed outlier: 3.681A pdb=" N VAL A 969 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1020 removed outlier: 3.974A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.827A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 removed outlier: 3.508A pdb=" N GLN A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.240A pdb=" N ARG A 78 " --> pdb=" O CYS A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.098A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 293 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.533A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.660A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.975A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A 504 " --> pdb=" O GLY A 869 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 768 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525 removed outlier: 4.903A pdb=" N VAL A 520 " --> pdb=" O ARG A 720 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG A 720 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 522 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 718 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 633 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 579 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 removed outlier: 3.503A pdb=" N SER A 557 " --> pdb=" O VAL A 564 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1302 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: 2.94 Time building geometry restraints manager: 2.11 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: 2163 1.33 - 1.45: 1028 1.45 - 1.57: 4280 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7536 Sorted by residual: bond pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 1.521 1.349 0.172 3.30e-02 9.18e+02 2.73e+01 bond pdb=" CB TYR A 935 " pdb=" CG TYR A 935 " ideal model delta sigma weight residual 1.512 1.437 0.075 2.20e-02 2.07e+03 1.17e+01 bond pdb=" C TYR A 935 " pdb=" N SER A 936 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.31e-02 5.83e+03 1.02e+01 bond pdb=" CG TYR A 935 " pdb=" CD1 TYR A 935 " ideal model delta sigma weight residual 1.389 1.328 0.061 2.10e-02 2.27e+03 8.55e+00 bond pdb=" CG GLN A 108 " pdb=" CD GLN A 108 " ideal model delta sigma weight residual 1.516 1.452 0.064 2.50e-02 1.60e+03 6.54e+00 ... (remaining 7531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 10178 2.28 - 4.57: 108 4.57 - 6.85: 13 6.85 - 9.14: 4 9.14 - 11.42: 1 Bond angle restraints: 10304 Sorted by residual: angle pdb=" CA TYR A 935 " pdb=" CB TYR A 935 " pdb=" CG TYR A 935 " ideal model delta sigma weight residual 113.90 105.40 8.50 1.80e+00 3.09e-01 2.23e+01 angle pdb=" CG1 VAL A 107 " pdb=" CB VAL A 107 " pdb=" CG2 VAL A 107 " ideal model delta sigma weight residual 110.80 102.10 8.70 2.20e+00 2.07e-01 1.57e+01 angle pdb=" CB LEU A 270 " pdb=" CG LEU A 270 " pdb=" CD2 LEU A 270 " ideal model delta sigma weight residual 110.70 122.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN A 108 " pdb=" CB GLN A 108 " pdb=" CG GLN A 108 " ideal model delta sigma weight residual 114.10 106.65 7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 107.75 112.37 -4.62 1.46e+00 4.69e-01 1.00e+01 ... (remaining 10299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4191 17.56 - 35.11: 269 35.11 - 52.67: 39 52.67 - 70.23: 6 70.23 - 87.79: 4 Dihedral angle restraints: 4509 sinusoidal: 1516 harmonic: 2993 Sorted by residual: dihedral pdb=" CA VAL A 964 " pdb=" C VAL A 964 " pdb=" N ILE A 965 " pdb=" CA ILE A 965 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU A 934 " pdb=" C LEU A 934 " pdb=" N TYR A 935 " pdb=" CA TYR A 935 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA SER A 889 " pdb=" C SER A 889 " pdb=" N LEU A 890 " pdb=" CA LEU A 890 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 1268 0.370 - 0.741: 0 0.741 - 1.111: 0 1.111 - 1.482: 0 1.482 - 1.852: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -0.74 -1.85 2.00e-01 2.50e+01 8.58e+01 chirality pdb=" CA TYR A 935 " pdb=" N TYR A 935 " pdb=" C TYR A 935 " pdb=" CB TYR A 935 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1266 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 934 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LEU A 934 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU A 934 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR A 935 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 935 " -0.028 2.00e-02 2.50e+03 2.77e-02 1.54e+01 pdb=" CG TYR A 935 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 935 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 935 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 935 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 935 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 935 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 935 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 107 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL A 107 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 107 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 108 " 0.015 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 72 2.64 - 3.20: 7035 3.20 - 3.77: 11463 3.77 - 4.33: 15443 4.33 - 4.90: 26475 Nonbonded interactions: 60488 Sorted by model distance: nonbonded pdb=" OH TYR A 359 " pdb=" OG1 THR A 368 " model vdw 2.074 3.040 nonbonded pdb=" OE2 GLU A 172 " pdb=" NE2 GLN A 175 " model vdw 2.159 3.120 nonbonded pdb=" NH1 ARG A 816 " pdb=" O PRO A1167 " model vdw 2.239 3.120 nonbonded pdb=" O ASP A 325 " pdb=" OG1 THR A 391 " model vdw 2.285 3.040 nonbonded pdb=" O PHE A 958 " pdb=" ND2 ASN A 962 " model vdw 2.311 3.120 ... (remaining 60483 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: 3.160 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.005 0.172 7536 Z= 0.339 Angle : 0.643 11.421 10304 Z= 0.341 Chirality : 0.068 1.852 1269 Planarity : 0.004 0.063 1316 Dihedral : 12.160 87.785 2575 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.22 (0.26), residues: 1024 helix: 0.65 (0.23), residues: 501 sheet: 0.25 (0.41), residues: 151 loop : -0.42 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 100 HIS 0.014 0.001 HIS A 364 PHE 0.024 0.002 PHE A 958 TYR 0.052 0.002 TYR A 935 ARG 0.012 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.776 Fit side-chains REVERT: A 761 MET cc_start: 0.8769 (mtt) cc_final: 0.8546 (mtt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.3428 time to fit residues: 72.8922 Evaluate side-chains 36 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 49 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 0.0770 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 939 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069278 restraints weight = 19092.417| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.76 r_work: 0.3106 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7536 Z= 0.186 Angle : 0.571 8.833 10304 Z= 0.285 Chirality : 0.042 0.142 1269 Planarity : 0.005 0.055 1316 Dihedral : 4.178 17.347 1099 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.84 % Allowed : 4.64 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.07 (0.26), residues: 1024 helix: 1.45 (0.23), residues: 503 sheet: 0.32 (0.42), residues: 153 loop : -0.03 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1166 HIS 0.002 0.001 HIS A 408 PHE 0.023 0.002 PHE A 958 TYR 0.024 0.001 TYR A 935 ARG 0.011 0.001 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.790 Fit side-chains REVERT: A 421 MET cc_start: 0.8827 (mmp) cc_final: 0.7951 (pp-130) REVERT: A 761 MET cc_start: 0.9214 (mtt) cc_final: 0.8895 (mtp) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.9460 time to fit residues: 45.3902 Evaluate side-chains 40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 1031 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.094568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066846 restraints weight = 19395.464| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.77 r_work: 0.3039 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7536 Z= 0.265 Angle : 0.549 9.272 10304 Z= 0.271 Chirality : 0.042 0.168 1269 Planarity : 0.004 0.050 1316 Dihedral : 4.019 16.998 1099 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.69 % Allowed : 6.61 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.37 (0.27), residues: 1024 helix: 1.70 (0.23), residues: 505 sheet: 0.28 (0.42), residues: 158 loop : 0.20 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 170 HIS 0.002 0.001 HIS A 831 PHE 0.020 0.002 PHE A 958 TYR 0.017 0.001 TYR A 935 ARG 0.015 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.804 Fit side-chains REVERT: A 421 MET cc_start: 0.8851 (mmp) cc_final: 0.7926 (pp-130) REVERT: A 761 MET cc_start: 0.9188 (mtt) cc_final: 0.8897 (mtt) outliers start: 12 outliers final: 4 residues processed: 46 average time/residue: 0.8046 time to fit residues: 40.9587 Evaluate side-chains 40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 1031 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 67.2012 > 50: distance: 36 - 59: 27.332 distance: 40 - 68: 30.199 distance: 55 - 59: 26.657 distance: 59 - 60: 29.062 distance: 60 - 61: 12.886 distance: 60 - 63: 30.797 distance: 61 - 62: 16.921 distance: 61 - 68: 5.754 distance: 63 - 64: 26.689 distance: 64 - 65: 32.616 distance: 65 - 66: 24.238 distance: 65 - 67: 33.417 distance: 68 - 69: 9.939 distance: 69 - 70: 14.235 distance: 70 - 71: 18.906 distance: 70 - 72: 28.361 distance: 72 - 73: 33.159 distance: 73 - 74: 17.456 distance: 73 - 76: 22.314 distance: 74 - 75: 3.108 distance: 74 - 80: 17.863 distance: 76 - 77: 8.924 distance: 76 - 78: 13.498 distance: 80 - 81: 21.173 distance: 80 - 204: 26.166 distance: 81 - 82: 22.901 distance: 81 - 84: 16.029 distance: 82 - 83: 48.167 distance: 82 - 91: 23.987 distance: 83 - 201: 36.059 distance: 84 - 85: 29.767 distance: 85 - 86: 19.036 distance: 85 - 87: 29.651 distance: 86 - 88: 49.036 distance: 87 - 89: 13.292 distance: 88 - 90: 9.693 distance: 89 - 90: 10.925 distance: 91 - 92: 7.082 distance: 92 - 93: 19.793 distance: 92 - 95: 35.147 distance: 93 - 94: 22.993 distance: 93 - 97: 16.356 distance: 95 - 96: 67.201 distance: 97 - 98: 24.355 distance: 98 - 99: 26.527 distance: 98 - 101: 5.042 distance: 99 - 105: 7.274 distance: 101 - 102: 14.320 distance: 101 - 103: 6.356 distance: 102 - 104: 12.502 distance: 105 - 106: 33.282 distance: 106 - 107: 15.252 distance: 106 - 109: 13.917 distance: 107 - 108: 26.475 distance: 107 - 115: 39.118 distance: 108 - 130: 33.012 distance: 109 - 110: 14.998 distance: 110 - 111: 24.884 distance: 110 - 112: 19.643 distance: 111 - 113: 16.501 distance: 112 - 114: 14.821 distance: 113 - 114: 15.777 distance: 115 - 116: 4.963 distance: 115 - 121: 23.806 distance: 116 - 117: 16.724 distance: 116 - 119: 19.373 distance: 117 - 118: 29.275 distance: 117 - 122: 19.294 distance: 118 - 141: 27.228 distance: 122 - 123: 9.372 distance: 123 - 124: 22.241 distance: 123 - 126: 13.561 distance: 124 - 125: 11.809 distance: 124 - 130: 15.249 distance: 126 - 127: 32.775 distance: 127 - 128: 21.002 distance: 127 - 129: 25.598 distance: 130 - 131: 22.095 distance: 131 - 132: 9.535 distance: 131 - 134: 23.006 distance: 132 - 133: 19.419 distance: 132 - 141: 15.880 distance: 133 - 156: 28.950 distance: 134 - 135: 9.873 distance: 135 - 136: 22.046 distance: 136 - 137: 5.209 distance: 137 - 138: 42.423 distance: 138 - 139: 27.387 distance: 138 - 140: 41.376