Starting phenix.real_space_refine on Thu Jul 2 02:01:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.cif" model { file = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phw_17677/07_2026/8phw_17677.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 36 5.16 5 C 3500 2.51 5 N 847 2.21 5 O 976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5359 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3528 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 15, 'TRANS': 438} Chain breaks: 7 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 972 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'FY5': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.20 Number of scatterers: 5359 At special positions: 0 Unit cell: (87.72, 94.86, 104.55, 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 36 16.00 O 976 8.00 N 847 7.00 C 3500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 0.27 Conformation dependent library (CDL) restraints added in 169.8 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 46.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 removed outlier: 3.742A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.860A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 4.217A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.612A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.718A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.743A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.891A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.153A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 257 through 274 removed outlier: 4.055A pdb=" N ASN A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.595A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N SER A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.875A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 3.522A pdb=" N ALA A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 527 through 559 removed outlier: 3.685A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 597 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 646 removed outlier: 3.665A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 435 removed outlier: 7.052A pdb=" N SER A 434 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A 520 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 removed outlier: 4.208A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 54 removed outlier: 6.837A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.777A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 750 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: 0.59 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 822 1.32 - 1.45: 1624 1.45 - 1.57: 2991 1.57 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 5491 Sorted by residual: bond pdb=" O20 FY5 A 701 " pdb=" S21 FY5 A 701 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.351 -0.020 7.90e-03 1.60e+04 6.28e+00 bond pdb=" C18 FY5 A 701 " pdb=" O20 FY5 A 701 " ideal model delta sigma weight residual 1.372 1.421 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" N VAL L 34 " pdb=" CA VAL L 34 " ideal model delta sigma weight residual 1.459 1.441 0.018 1.25e-02 6.40e+03 2.09e+00 bond pdb=" C SER H 36 " pdb=" N ILE H 37 " ideal model delta sigma weight residual 1.334 1.316 0.017 1.24e-02 6.50e+03 1.98e+00 ... (remaining 5486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 7000 1.36 - 2.72: 372 2.72 - 4.07: 56 4.07 - 5.43: 18 5.43 - 6.79: 6 Bond angle restraints: 7452 Sorted by residual: angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 112.83 108.67 4.16 9.90e-01 1.02e+00 1.77e+01 angle pdb=" N TYR H 63 " pdb=" CA TYR H 63 " pdb=" C TYR H 63 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.93e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 119.01 -5.11 1.80e+00 3.09e-01 8.05e+00 angle pdb=" C ASN A 403 " pdb=" CA ASN A 403 " pdb=" CB ASN A 403 " ideal model delta sigma weight residual 110.42 115.50 -5.08 1.99e+00 2.53e-01 6.51e+00 ... (remaining 7447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.98: 2730 11.98 - 23.96: 278 23.96 - 35.94: 107 35.94 - 47.92: 36 47.92 - 59.90: 11 Dihedral angle restraints: 3162 sinusoidal: 1199 harmonic: 1963 Sorted by residual: dihedral pdb=" CA CYS A 607 " pdb=" C CYS A 607 " pdb=" N GLY A 608 " pdb=" CA GLY A 608 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N THR A 609 " pdb=" CA THR A 609 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N SER A 618 " pdb=" CA SER A 618 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 3159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 496 0.029 - 0.058: 229 0.058 - 0.087: 76 0.087 - 0.115: 37 0.115 - 0.144: 9 Chirality restraints: 847 Sorted by residual: chirality pdb=" CA VAL A 473 " pdb=" N VAL A 473 " pdb=" C VAL A 473 " pdb=" CB VAL A 473 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA THR A 186 " pdb=" N THR A 186 " pdb=" C THR A 186 " pdb=" CB THR A 186 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PRO A 220 " pdb=" N PRO A 220 " pdb=" C PRO A 220 " pdb=" CB PRO A 220 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 844 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 219 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO A 220 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 106 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 107 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 590 " -0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 590 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 590 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 590 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 590 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 590 " -0.001 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 793 2.75 - 3.29: 5508 3.29 - 3.82: 8421 3.82 - 4.36: 9687 4.36 - 4.90: 16556 Nonbonded interactions: 40965 Sorted by model distance: nonbonded pdb=" O CYS A 101 " pdb=" OG SER A 269 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 415 " pdb=" OG SER A 418 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG H 70 " pdb=" O SER H 88 " model vdw 2.248 3.120 nonbonded pdb=" O CYS A 474 " pdb=" N ALA A 519 " model vdw 2.252 3.120 ... (remaining 40960 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: 10.560 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.930 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 0.070 5497 Z= 0.233 Angle : 0.723 6.790 7464 Z= 0.423 Chirality : 0.041 0.144 847 Planarity : 0.005 0.058 905 Dihedral : 12.493 59.901 1898 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.20 % Allowed : 7.75 % Favored : 86.06 % 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: -3.65 (0.26), residues: 669 helix: -1.77 (0.25), residues: 283 sheet: -1.50 (0.57), residues: 81 loop : -3.36 (0.26), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 70 TYR 0.025 0.002 TYR A 590 PHE 0.010 0.001 PHE A 537 TRP 0.014 0.002 TRP A 254 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 ( 5491) covalent geometry : angle 0.72217 / 0.42 ( 7452) SS BOND : bond 0.00428 / 0.31 ( 6) SS BOND : angle 1.12052 / 0.55 ( 12) hydrogen bonds : bond 0.13904 / 9.20 ( 256) hydrogen bonds : angle 5.86732 / 4.15 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6160 (ttp80) REVERT: A 170 MET cc_start: 0.7729 (ttm) cc_final: 0.7378 (ttm) REVERT: A 218 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (tt) REVERT: A 253 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6436 (mtm110) REVERT: A 386 PHE cc_start: 0.8258 (t80) cc_final: 0.7730 (t80) REVERT: A 390 MET cc_start: 0.7207 (mtm) cc_final: 0.6897 (mtm) REVERT: A 417 MET cc_start: 0.6765 (mmm) cc_final: 0.6395 (mmm) REVERT: A 601 LYS cc_start: 0.7751 (tttp) cc_final: 0.7317 (tttp) REVERT: A 631 MET cc_start: 0.6745 (tpp) cc_final: 0.6223 (tpp) REVERT: H 32 PHE cc_start: 0.8359 (t80) cc_final: 0.8126 (t80) REVERT: L 18 ASP cc_start: 0.5539 (m-30) cc_final: 0.5334 (m-30) REVERT: L 43 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7601 (mmtm) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.0609 time to fit residues: 13.5827 Evaluate side-chains 147 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123989 restraints weight = 9171.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127920 restraints weight = 4518.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130466 restraints weight = 2783.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132074 restraints weight = 1990.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133272 restraints weight = 1585.103| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5497 Z= 0.142 Angle : 0.606 7.553 7464 Z= 0.312 Chirality : 0.042 0.247 847 Planarity : 0.005 0.058 905 Dihedral : 8.386 58.687 793 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.37 % Allowed : 14.80 % Favored : 78.83 % 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: -1.69 (0.30), residues: 669 helix: 0.30 (0.29), residues: 296 sheet: -1.02 (0.60), residues: 78 loop : -2.72 (0.29), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.015 0.001 TYR A 625 PHE 0.022 0.001 PHE A 73 TRP 0.009 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 5491) covalent geometry : angle 0.60482 / 0.31 ( 7452) SS BOND : bond 0.00421 / 0.31 ( 6) SS BOND : angle 1.24473 / 0.63 ( 12) hydrogen bonds : bond 0.04772 / 3.10 ( 256) hydrogen bonds : angle 4.52252 / 3.34 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.7681 (ttm) cc_final: 0.7467 (ttm) REVERT: A 173 TYR cc_start: 0.7477 (m-80) cc_final: 0.7238 (m-80) REVERT: A 217 MET cc_start: 0.7921 (mmp) cc_final: 0.7514 (mmp) REVERT: A 253 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6596 (mtm110) REVERT: A 386 PHE cc_start: 0.8091 (t80) cc_final: 0.7397 (t80) REVERT: A 390 MET cc_start: 0.7096 (mtm) cc_final: 0.6779 (mtm) REVERT: A 404 THR cc_start: 0.6277 (OUTLIER) cc_final: 0.5964 (m) REVERT: A 416 VAL cc_start: 0.7325 (t) cc_final: 0.7124 (p) REVERT: A 417 MET cc_start: 0.6615 (mmm) cc_final: 0.6301 (mmm) REVERT: A 533 LYS cc_start: 0.7948 (mttm) cc_final: 0.7695 (mttm) REVERT: A 545 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7877 (mm) REVERT: A 601 LYS cc_start: 0.7615 (tttp) cc_final: 0.7214 (tttp) REVERT: A 631 MET cc_start: 0.6754 (tpp) cc_final: 0.6232 (tpp) REVERT: H 32 PHE cc_start: 0.8296 (t80) cc_final: 0.8033 (t80) REVERT: L 18 ASP cc_start: 0.6022 (m-30) cc_final: 0.5712 (m-30) REVERT: L 43 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7495 (mmtm) outliers start: 37 outliers final: 19 residues processed: 157 average time/residue: 0.0514 time to fit residues: 11.0275 Evaluate side-chains 148 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.8333 > 50: distance: 40 - 143: 18.747 distance: 43 - 140: 18.759 distance: 67 - 74: 27.403 distance: 74 - 75: 16.899 distance: 75 - 76: 7.909 distance: 75 - 78: 18.071 distance: 76 - 77: 24.961 distance: 76 - 83: 4.042 distance: 78 - 79: 13.487 distance: 79 - 80: 12.449 distance: 80 - 81: 18.527 distance: 81 - 82: 23.470 distance: 83 - 84: 14.804 distance: 83 - 89: 22.333 distance: 84 - 85: 21.040 distance: 84 - 87: 15.399 distance: 85 - 86: 21.786 distance: 85 - 90: 13.795 distance: 87 - 88: 21.973 distance: 88 - 89: 17.982 distance: 90 - 91: 10.761 distance: 91 - 92: 24.321 distance: 92 - 93: 16.549 distance: 92 - 94: 8.330 distance: 94 - 95: 43.102 distance: 95 - 96: 17.592 distance: 95 - 98: 17.451 distance: 96 - 97: 4.896 distance: 96 - 103: 49.797 distance: 98 - 99: 31.354 distance: 99 - 100: 36.661 distance: 100 - 101: 28.498 distance: 101 - 102: 5.971 distance: 103 - 104: 20.696 distance: 104 - 105: 23.073 distance: 104 - 107: 12.504 distance: 105 - 106: 38.095 distance: 105 - 108: 14.300 distance: 108 - 109: 12.998 distance: 108 - 114: 23.329 distance: 109 - 110: 22.073 distance: 109 - 112: 13.698 distance: 110 - 111: 12.644 distance: 110 - 115: 19.621 distance: 112 - 113: 17.790 distance: 113 - 114: 22.821 distance: 115 - 116: 6.426 distance: 116 - 117: 14.260 distance: 116 - 119: 20.047 distance: 117 - 118: 33.864 distance: 117 - 124: 5.592 distance: 119 - 120: 15.580 distance: 120 - 121: 9.105 distance: 121 - 122: 25.221 distance: 122 - 123: 11.886 distance: 124 - 125: 9.069 distance: 125 - 126: 5.098 distance: 125 - 128: 26.674 distance: 126 - 127: 28.136 distance: 126 - 132: 28.191 distance: 128 - 129: 24.053 distance: 129 - 130: 10.968 distance: 129 - 131: 9.553 distance: 132 - 133: 22.300 distance: 133 - 134: 14.742 distance: 133 - 136: 26.410 distance: 134 - 135: 9.759 distance: 134 - 140: 10.716 distance: 136 - 137: 15.019 distance: 137 - 138: 28.187 distance: 137 - 139: 26.829 distance: 140 - 141: 6.941 distance: 141 - 142: 11.638 distance: 141 - 144: 20.944 distance: 142 - 143: 13.219 distance: 142 - 148: 8.519 distance: 144 - 145: 20.429 distance: 144 - 146: 17.708 distance: 145 - 147: 21.717