Starting phenix.real_space_refine on Tue Feb 3 17:43:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yck_72775/02_2026/9yck_72775.map" } resolution = 2.8 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 3475 2.51 5 N 963 2.21 5 O 1141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5661 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 971 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "B" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4009 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 28, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 675 Classifications: {'RNA': 32} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 74 36.602 52.614 31.085 1.00 45.35 S ATOM 553 SG CYS A 77 33.804 50.264 29.888 1.00 44.67 S ATOM 651 SG CYS A 90 33.984 53.848 28.510 1.00 57.10 S ATOM 859 SG CYS A 117 44.125 69.621 21.973 1.00 85.15 S ATOM 880 SG CYS A 120 45.224 68.050 18.727 1.00 84.50 S ATOM 949 SG CYS A 128 47.770 68.923 21.467 1.00 89.83 S ATOM 963 SG CYS A 130 46.260 71.648 19.388 1.00 99.65 S ATOM 2576 SG CYS B 207 37.346 60.651 63.114 1.00 52.92 S ATOM 2596 SG CYS B 210 38.667 60.653 66.713 1.00 54.06 S ATOM 2718 SG CYS B 226 36.373 57.876 65.565 1.00 58.88 S ATOM 3017 SG CYS B 261 27.174 26.657 71.782 1.00 60.14 S ATOM 3147 SG CYS B 279 29.985 28.909 70.219 1.00 58.71 S ATOM 4522 SG CYS B 448 41.480 51.900 116.235 1.00157.21 S ATOM 4605 SG CYS B 474 37.751 52.063 116.752 1.00154.21 S ATOM 4647 SG CYS B 481 39.366 54.387 114.162 1.00151.35 S Time building chain proxies: 1.43, per 1000 atoms: 0.25 Number of scatterers: 5661 At special positions: 0 Unit cell: (70.8804, 83.1313, 128.635, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 44 16.00 P 32 15.00 Mg 1 11.99 O 1141 8.00 N 963 7.00 C 3475 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: 0.52 Conformation dependent library (CDL) restraints added in 329.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 207 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 261 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 484 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 474 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 448 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 481 " Number of angles added : 17 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 31.1% alpha, 16.7% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.572A pdb=" N LEU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.727A pdb=" N GLY A 88 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 89 " --> pdb=" O VAL A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 143 through 155 removed outlier: 3.502A pdb=" N PHE B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 147 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS B 148 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.593A pdb=" N HIS B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 175 Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.800A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.609A pdb=" N SER B 230 " --> pdb=" O TRP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.667A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 301 through 323 removed outlier: 3.669A pdb=" N ARG B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.528A pdb=" N ALA B 374 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 376 " --> pdb=" O PHE B 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 376' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.738A pdb=" N GLY B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 502 removed outlier: 3.719A pdb=" N GLU B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.296A pdb=" N VAL B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.649A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 108 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.649A pdb=" N VAL B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN B 104 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 96 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 108 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 87 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA6, first strand: chain 'B' and resid 360 through 361 removed outlier: 9.226A pdb=" N GLN B 361 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 350 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP B 381 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 442 through 443 removed outlier: 6.175A pdb=" N TYR B 442 " --> pdb=" O ILE B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 165 hydrogen bonds defined for protein. 444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1612 1.34 - 1.46: 1306 1.46 - 1.57: 2839 1.57 - 1.69: 62 1.69 - 1.81: 53 Bond restraints: 5872 Sorted by residual: bond pdb=" N GLY A 50 " pdb=" CA GLY A 50 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.11e+01 bond pdb=" C ASP B 343 " pdb=" N PRO B 344 " ideal model delta sigma weight residual 1.335 1.362 -0.027 8.70e-03 1.32e+04 9.89e+00 bond pdb=" N ASP B 37 " pdb=" CA ASP B 37 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.12e-02 7.97e+03 9.61e+00 bond pdb=" N GLU B 367 " pdb=" CA GLU B 367 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.00e+00 bond pdb=" N LEU B 45 " pdb=" CA LEU B 45 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.16e-02 7.43e+03 8.50e+00 ... (remaining 5867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 7658 1.36 - 2.72: 384 2.72 - 4.08: 64 4.08 - 5.44: 17 5.44 - 6.80: 14 Bond angle restraints: 8137 Sorted by residual: angle pdb=" N ASN B 44 " pdb=" CA ASN B 44 " pdb=" C ASN B 44 " ideal model delta sigma weight residual 113.20 108.56 4.64 1.21e+00 6.83e-01 1.47e+01 angle pdb=" N ILE B 287 " pdb=" CA ILE B 287 " pdb=" C ILE B 287 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 angle pdb=" C ASP B 273 " pdb=" CA ASP B 273 " pdb=" CB ASP B 273 " ideal model delta sigma weight residual 110.79 116.41 -5.62 1.66e+00 3.63e-01 1.14e+01 angle pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " ideal model delta sigma weight residual 112.60 115.91 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N GLU B 92 " pdb=" CA GLU B 92 " pdb=" C GLU B 92 " ideal model delta sigma weight residual 110.52 105.82 4.70 1.48e+00 4.57e-01 1.01e+01 ... (remaining 8132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.44: 3221 22.44 - 44.88: 187 44.88 - 67.31: 61 67.31 - 89.75: 10 89.75 - 112.19: 1 Dihedral angle restraints: 3480 sinusoidal: 1624 harmonic: 1856 Sorted by residual: dihedral pdb=" CA ASP B 343 " pdb=" C ASP B 343 " pdb=" N PRO B 344 " pdb=" CA PRO B 344 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU B 363 " pdb=" C LEU B 363 " pdb=" N PHE B 364 " pdb=" CA PHE B 364 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CB GLU A 6 " pdb=" CG GLU A 6 " pdb=" CD GLU A 6 " pdb=" OE1 GLU A 6 " ideal model delta sinusoidal sigma weight residual 0.00 85.08 -85.08 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 3477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 869 0.113 - 0.226: 34 0.226 - 0.340: 1 0.340 - 0.453: 4 0.453 - 0.566: 5 Chirality restraints: 913 Sorted by residual: chirality pdb=" P G C 24 " pdb=" OP1 G C 24 " pdb=" OP2 G C 24 " pdb=" O5' G C 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P U C 6 " pdb=" OP1 U C 6 " pdb=" OP2 U C 6 " pdb=" O5' U C 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" P U C 25 " pdb=" OP1 U C 25 " pdb=" OP2 U C 25 " pdb=" O5' U C 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 910 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 326 " -0.014 2.00e-02 2.50e+03 1.55e-02 4.22e+00 pdb=" CG PHE B 326 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 326 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 326 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 326 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 326 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 326 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 38 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C GLU B 38 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU B 38 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 39 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 380 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C PHE B 380 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 380 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP B 381 " 0.010 2.00e-02 2.50e+03 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 87 2.66 - 3.22: 4858 3.22 - 3.78: 8954 3.78 - 4.34: 12650 4.34 - 4.90: 19630 Nonbonded interactions: 46179 Sorted by model distance: nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.102 2.170 nonbonded pdb=" O ALA A 8 " pdb=" OG SER A 11 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP B 273 " pdb="MG MG B 601 " model vdw 2.252 2.170 nonbonded pdb=" NZ LYS B 71 " pdb=" O PHE B 73 " model vdw 2.306 3.120 nonbonded pdb=" O LEU B 497 " pdb=" OG SER B 501 " model vdw 2.312 3.040 ... (remaining 46174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.270 Find NCS groups from input model: 0.020 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:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.004 0.039 5892 Z= 0.268 Angle : 0.742 6.801 8154 Z= 0.442 Chirality : 0.067 0.566 913 Planarity : 0.005 0.042 932 Dihedral : 15.691 112.191 2292 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % 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 are not related in a simple way. whole: -0.43 (0.32), residues: 630 helix: -0.03 (0.39), residues: 151 sheet: -0.07 (0.56), residues: 82 loop : -0.37 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.010 0.001 TYR B 491 PHE 0.036 0.002 PHE B 326 TRP 0.009 0.001 TRP A 123 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5872) covalent geometry : angle 0.73690 ( 8137) hydrogen bonds : bond 0.17722 ( 193) hydrogen bonds : angle 6.55653 ( 508) metal coordination : bond 0.00586 ( 20) metal coordination : angle 2.04403 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.225 Fit side-chains REVERT: B 76 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7783 (ttt-90) REVERT: B 97 SER cc_start: 0.8427 (p) cc_final: 0.8209 (m) REVERT: B 306 ASN cc_start: 0.7840 (m-40) cc_final: 0.7464 (m-40) REVERT: B 495 TYR cc_start: 0.8175 (t80) cc_final: 0.7344 (t80) outliers start: 0 outliers final: 1 residues processed: 110 average time/residue: 0.6186 time to fit residues: 70.6802 Evaluate side-chains 104 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 82 GLN B 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102914 restraints weight = 7337.434| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.61 r_work: 0.3228 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5892 Z= 0.157 Angle : 0.519 7.259 8154 Z= 0.261 Chirality : 0.042 0.138 913 Planarity : 0.005 0.035 932 Dihedral : 13.244 120.503 1175 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.21 % Allowed : 13.24 % Favored : 84.56 % 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 are not related in a simple way. whole: -0.11 (0.33), residues: 630 helix: 0.65 (0.39), residues: 160 sheet: -0.22 (0.56), residues: 82 loop : -0.29 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.013 0.001 TYR B 427 PHE 0.010 0.001 PHE B 326 TRP 0.012 0.001 TRP A 123 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5872) covalent geometry : angle 0.50466 ( 8137) hydrogen bonds : bond 0.05145 ( 193) hydrogen bonds : angle 4.33443 ( 508) metal coordination : bond 0.00635 ( 20) metal coordination : angle 2.68774 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.123 Fit side-chains REVERT: A 57 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8598 (t) REVERT: B 76 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7791 (ttt-90) REVERT: B 90 ASP cc_start: 0.8074 (t70) cc_final: 0.7859 (t0) REVERT: B 97 SER cc_start: 0.8451 (p) cc_final: 0.8169 (m) REVERT: B 303 LYS cc_start: 0.8113 (tttt) cc_final: 0.7880 (mtpp) REVERT: B 495 TYR cc_start: 0.8389 (t80) cc_final: 0.7680 (t80) outliers start: 12 outliers final: 3 residues processed: 117 average time/residue: 0.5475 time to fit residues: 66.6409 Evaluate side-chains 110 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 222 GLN B 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102604 restraints weight = 7232.525| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.58 r_work: 0.3224 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5892 Z= 0.165 Angle : 0.507 7.946 8154 Z= 0.255 Chirality : 0.042 0.134 913 Planarity : 0.004 0.033 932 Dihedral : 12.826 119.578 1173 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.84 % Allowed : 13.05 % Favored : 85.11 % 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 are not related in a simple way. whole: -0.00 (0.33), residues: 630 helix: 0.86 (0.39), residues: 160 sheet: -0.10 (0.57), residues: 82 loop : -0.29 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 84 TYR 0.011 0.001 TYR B 350 PHE 0.016 0.001 PHE B 326 TRP 0.012 0.001 TRP B 381 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5872) covalent geometry : angle 0.49131 ( 8137) hydrogen bonds : bond 0.05097 ( 193) hydrogen bonds : angle 4.18791 ( 508) metal coordination : bond 0.00623 ( 20) metal coordination : angle 2.81444 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.253 Fit side-chains REVERT: B 76 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7856 (ttt-90) REVERT: B 97 SER cc_start: 0.8438 (p) cc_final: 0.8177 (m) REVERT: B 303 LYS cc_start: 0.8076 (tttt) cc_final: 0.7862 (mtpp) REVERT: B 367 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 471 ILE cc_start: 0.8392 (mp) cc_final: 0.8146 (mm) REVERT: B 495 TYR cc_start: 0.8400 (t80) cc_final: 0.7665 (t80) outliers start: 10 outliers final: 4 residues processed: 105 average time/residue: 0.7330 time to fit residues: 79.7160 Evaluate side-chains 106 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 222 GLN B 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102859 restraints weight = 7314.828| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.60 r_work: 0.3227 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5892 Z= 0.160 Angle : 0.497 8.314 8154 Z= 0.250 Chirality : 0.041 0.134 913 Planarity : 0.004 0.032 932 Dihedral : 12.733 117.052 1173 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.02 % Allowed : 13.79 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.33), residues: 630 helix: 0.94 (0.39), residues: 160 sheet: -0.12 (0.57), residues: 82 loop : -0.31 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.017 0.001 TYR B 350 PHE 0.012 0.001 PHE B 326 TRP 0.011 0.001 TRP A 123 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5872) covalent geometry : angle 0.47968 ( 8137) hydrogen bonds : bond 0.04766 ( 193) hydrogen bonds : angle 4.09001 ( 508) metal coordination : bond 0.00566 ( 20) metal coordination : angle 2.89738 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.208 Fit side-chains REVERT: B 76 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7829 (ttt-90) REVERT: B 87 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 97 SER cc_start: 0.8436 (p) cc_final: 0.8186 (m) REVERT: B 367 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 495 TYR cc_start: 0.8421 (t80) cc_final: 0.7763 (t80) outliers start: 11 outliers final: 4 residues processed: 111 average time/residue: 0.6712 time to fit residues: 77.3902 Evaluate side-chains 111 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 222 GLN B 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102758 restraints weight = 7347.500| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.61 r_work: 0.3223 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5892 Z= 0.166 Angle : 0.503 8.505 8154 Z= 0.253 Chirality : 0.041 0.134 913 Planarity : 0.004 0.033 932 Dihedral : 12.677 114.566 1173 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.47 % Allowed : 14.52 % Favored : 84.01 % 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 are not related in a simple way. whole: -0.01 (0.33), residues: 630 helix: 0.97 (0.39), residues: 159 sheet: -0.15 (0.56), residues: 82 loop : -0.34 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.026 0.001 TYR B 350 PHE 0.017 0.001 PHE B 326 TRP 0.011 0.001 TRP A 123 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5872) covalent geometry : angle 0.48593 ( 8137) hydrogen bonds : bond 0.04663 ( 193) hydrogen bonds : angle 4.08449 ( 508) metal coordination : bond 0.00592 ( 20) metal coordination : angle 2.92178 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.207 Fit side-chains REVERT: B 76 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7796 (ttt-90) REVERT: B 97 SER cc_start: 0.8413 (p) cc_final: 0.8164 (m) REVERT: B 495 TYR cc_start: 0.8415 (t80) cc_final: 0.7695 (t80) outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.6863 time to fit residues: 79.7419 Evaluate side-chains 111 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 487 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 68.6898 > 50: distance: 36 - 59: 37.188 distance: 42 - 45: 30.555 distance: 45 - 46: 50.586 distance: 46 - 47: 41.608 distance: 46 - 49: 7.541 distance: 47 - 51: 39.934 distance: 49 - 50: 18.585 distance: 50 - 146: 28.154 distance: 52 - 53: 18.322 distance: 52 - 55: 39.283 distance: 53 - 54: 8.157 distance: 53 - 59: 44.848 distance: 55 - 56: 25.225 distance: 56 - 57: 14.179 distance: 56 - 58: 26.837 distance: 59 - 60: 40.124 distance: 60 - 61: 60.402 distance: 60 - 63: 47.701 distance: 61 - 62: 52.996 distance: 61 - 67: 41.960 distance: 63 - 64: 41.078 distance: 67 - 68: 34.470 distance: 68 - 69: 41.027 distance: 69 - 70: 40.043 distance: 69 - 71: 38.688 distance: 71 - 72: 34.767 distance: 72 - 73: 40.156 distance: 73 - 74: 18.207 distance: 73 - 75: 9.779 distance: 75 - 76: 7.805 distance: 76 - 79: 23.796 distance: 80 - 81: 40.098 distance: 81 - 82: 38.729 distance: 81 - 84: 40.082 distance: 82 - 83: 40.240 distance: 82 - 87: 39.875 distance: 87 - 88: 32.602 distance: 88 - 89: 32.873 distance: 88 - 91: 32.684 distance: 89 - 90: 25.940 distance: 89 - 93: 16.203 distance: 90 - 123: 30.585 distance: 91 - 92: 6.145 distance: 92 - 146: 33.149 distance: 93 - 94: 59.323 distance: 94 - 95: 44.754 distance: 95 - 96: 44.161 distance: 95 - 104: 43.871 distance: 96 - 128: 31.109 distance: 98 - 99: 38.471 distance: 99 - 100: 6.415 distance: 100 - 101: 15.229 distance: 101 - 102: 12.599 distance: 101 - 103: 47.197 distance: 105 - 106: 39.668 distance: 105 - 108: 40.747 distance: 106 - 107: 39.228 distance: 106 - 113: 35.607 distance: 108 - 109: 41.339 distance: 109 - 110: 4.592 distance: 110 - 111: 40.418 distance: 111 - 112: 37.099