Starting phenix.real_space_refine on Wed Jul 1 21:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zs5_11388/07_2026/6zs5_11388.cif" } resolution = 3.5 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= 0.082 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 21 5.16 5 C 1261 2.51 5 N 341 2.21 5 O 413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 2036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1036 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 12} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.54, per 1000 atoms: 0.27 Number of scatterers: 2036 At special positions: 0 Unit cell: (72.628, 71.544, 88.888, 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 21 16.00 O 413 8.00 N 341 7.00 C 1261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 389 " distance=2.04 Simple disulfide: pdb=" SG CYS D 506 " - pdb=" SG CYS D 566 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 582 " distance=1.59 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 578 " distance=1.89 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A 396 " " NAG C 1 " - " ASN D 513 " Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 43.5 milliseconds 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.661A pdb=" N VAL A 342 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.680A pdb=" N TYR D 563 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 508 " --> pdb=" O TYR D 563 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS D 565 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS D 506 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 567 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 506 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440 removed outlier: 6.863A pdb=" N ALA A 438 " --> pdb=" O VAL D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 458 through 463 removed outlier: 4.017A pdb=" N TYR D 486 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 550 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG D 547 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 538 " --> pdb=" O ARG D 547 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 162 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: 0.15 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 332 1.31 - 1.44: 558 1.44 - 1.57: 1145 1.57 - 1.70: 3 1.70 - 1.83: 31 Bond restraints: 2069 Sorted by residual: bond pdb=" CA SER D 583 " pdb=" C SER D 583 " ideal model delta sigma weight residual 1.520 1.462 0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C SER D 583 " pdb=" O SER D 583 " ideal model delta sigma weight residual 1.234 1.180 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" CA SER D 583 " pdb=" CB SER D 583 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 1.460 1.423 0.036 1.20e-02 6.94e+03 9.24e+00 ... (remaining 2064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 2659 2.18 - 4.37: 101 4.37 - 6.55: 28 6.55 - 8.74: 3 8.74 - 10.92: 1 Bond angle restraints: 2792 Sorted by residual: angle pdb=" C LYS D 579 " pdb=" N PRO D 580 " pdb=" CA PRO D 580 " ideal model delta sigma weight residual 119.76 125.33 -5.57 1.03e+00 9.43e-01 2.92e+01 angle pdb=" N GLY A 387 " pdb=" CA GLY A 387 " pdb=" C GLY A 387 " ideal model delta sigma weight residual 112.34 123.26 -10.92 2.04e+00 2.40e-01 2.87e+01 angle pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 108.02 100.12 7.90 1.75e+00 3.27e-01 2.04e+01 angle pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta sigma weight residual 110.74 104.22 6.52 1.61e+00 3.86e-01 1.64e+01 angle pdb=" CA PRO D 580 " pdb=" C PRO D 580 " pdb=" N THR D 581 " ideal model delta sigma weight residual 115.56 110.66 4.90 1.27e+00 6.20e-01 1.49e+01 ... (remaining 2787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 1085 17.90 - 35.79: 87 35.79 - 53.69: 15 53.69 - 71.59: 4 71.59 - 89.48: 2 Dihedral angle restraints: 1193 sinusoidal: 472 harmonic: 721 Sorted by residual: dihedral pdb=" CA LYS A 346 " pdb=" C LYS A 346 " pdb=" N CYS A 347 " pdb=" CA CYS A 347 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual 123.40 109.35 14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C THR D 581 " pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual -122.00 -108.06 -13.94 0 2.50e+00 1.60e-01 3.11e+01 ... (remaining 1190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 256 0.068 - 0.137: 68 0.137 - 0.205: 4 0.205 - 0.273: 3 0.273 - 0.342: 2 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA THR D 581 " pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CB THR D 581 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C2 BMA B 3 " pdb=" C1 BMA B 3 " pdb=" C3 BMA B 3 " pdb=" O2 BMA B 3 " both_signs ideal model delta sigma weight residual False 2.47 2.74 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 330 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 525 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" CG ASP D 525 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP D 525 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP D 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 386 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP A 386 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 386 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 386 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 387 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 388 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.035 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 186 2.74 - 3.28: 1655 3.28 - 3.82: 2977 3.82 - 4.36: 3207 4.36 - 4.90: 5904 Nonbonded interactions: 13929 Sorted by model distance: nonbonded pdb=" O THR D 581 " pdb=" OG1 THR D 581 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP D 532 " pdb=" OG1 THR D 534 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OD1 ASN A 404 " model vdw 2.342 3.040 nonbonded pdb=" OG SER D 543 " pdb=" N SER D 544 " model vdw 2.348 3.120 nonbonded pdb=" OH TYR A 402 " pdb=" OD2 ASP D 495 " model vdw 2.369 3.040 ... (remaining 13924 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.620 Find NCS groups from input model: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.013 0.438 2081 Z= 0.660 Angle : 1.367 22.944 2823 Z= 0.691 Chirality : 0.067 0.342 333 Planarity : 0.008 0.061 352 Dihedral : 13.945 89.480 722 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Cbeta Deviations : 0.44 % 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: -2.98 (0.45), residues: 253 helix: None (None), residues: 0 sheet: -1.19 (0.53), residues: 92 loop : -2.61 (0.37), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.027 0.003 TYR D 486 PHE 0.024 0.003 PHE A 423 TRP 0.013 0.003 TRP A 377 HIS 0.002 0.001 HIS D 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.43 ( 2069) covalent geometry : angle 1.08744 / 0.59 ( 2792) SS BOND : bond 0.20505 / 10.46 ( 5) SS BOND : angle 11.03486 / 5.55 ( 10) hydrogen bonds : bond 0.28007 / 19.08 ( 53) hydrogen bonds : angle 10.55124 / 6.78 ( 162) link_ALPHA1-3 : bond 0.00788 / 0.41 ( 1) link_ALPHA1-3 : angle 1.61819 / 0.86 ( 3) link_ALPHA1-6 : bond 0.01075 / 0.57 ( 1) link_ALPHA1-6 : angle 1.86495 / 0.86 ( 3) link_BETA1-4 : bond 0.02124 / 1.03 ( 3) link_BETA1-4 : angle 6.23863 / 2.74 ( 9) link_NAG-ASN : bond 0.00391 / 0.19 ( 2) link_NAG-ASN : angle 8.07290 / 3.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.048 Fit side-chains REVERT: A 375 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6696 (tpt170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0647 time to fit residues: 4.5389 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.072262 restraints weight = 6035.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074077 restraints weight = 3318.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075364 restraints weight = 2215.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076194 restraints weight = 1679.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076824 restraints weight = 1393.818| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2081 Z= 0.160 Angle : 0.811 11.616 2823 Z= 0.381 Chirality : 0.047 0.169 333 Planarity : 0.005 0.046 352 Dihedral : 5.523 25.621 279 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.65 % Allowed : 22.33 % Favored : 73.02 % 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: -2.23 (0.47), residues: 253 helix: None (None), residues: 0 sheet: -0.43 (0.51), residues: 98 loop : -2.32 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.015 0.001 TYR D 486 PHE 0.010 0.001 PHE D 548 TRP 0.009 0.002 TRP A 377 HIS 0.001 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 2069) covalent geometry : angle 0.70819 / 0.36 ( 2792) SS BOND : bond 0.00252 / 0.13 ( 5) SS BOND : angle 1.02823 / 0.44 ( 10) hydrogen bonds : bond 0.04360 / 2.86 ( 53) hydrogen bonds : angle 6.72761 / 4.24 ( 162) link_ALPHA1-3 : bond 0.00665 / 0.35 ( 1) link_ALPHA1-3 : angle 1.06540 / 0.62 ( 3) link_ALPHA1-6 : bond 0.01372 / 0.72 ( 1) link_ALPHA1-6 : angle 1.88008 / 0.78 ( 3) link_BETA1-4 : bond 0.01967 / 0.94 ( 3) link_BETA1-4 : angle 4.76313 / 2.11 ( 9) link_NAG-ASN : bond 0.00337 / 0.18 ( 2) link_NAG-ASN : angle 6.18406 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.047 Fit side-chains REVERT: A 375 ARG cc_start: 0.7394 (mtp180) cc_final: 0.6608 (tpt170) REVERT: A 420 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7679 (ptmt) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.0476 time to fit residues: 2.8064 Evaluate side-chains 46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN D 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.084529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071228 restraints weight = 6178.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073128 restraints weight = 3364.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074369 restraints weight = 2225.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075260 restraints weight = 1689.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075824 restraints weight = 1394.301| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2081 Z= 0.173 Angle : 0.779 11.848 2823 Z= 0.370 Chirality : 0.047 0.180 333 Planarity : 0.005 0.044 352 Dihedral : 5.201 23.506 279 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.51 % Allowed : 20.47 % Favored : 73.02 % 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: -1.96 (0.48), residues: 253 helix: None (None), residues: 0 sheet: -0.17 (0.50), residues: 96 loop : -2.16 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.019 0.002 TYR D 486 PHE 0.011 0.001 PHE A 423 TRP 0.008 0.002 TRP A 377 HIS 0.001 0.001 HIS D 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 2069) covalent geometry : angle 0.68600 / 0.35 ( 2792) SS BOND : bond 0.00105 / 0.05 ( 5) SS BOND : angle 0.82685 / 0.33 ( 10) hydrogen bonds : bond 0.04284 / 2.74 ( 53) hydrogen bonds : angle 6.15936 / 3.94 ( 162) link_ALPHA1-3 : bond 0.00673 / 0.35 ( 1) link_ALPHA1-3 : angle 1.18143 / 0.69 ( 3) link_ALPHA1-6 : bond 0.00983 / 0.52 ( 1) link_ALPHA1-6 : angle 1.70964 / 0.75 ( 3) link_BETA1-4 : bond 0.01780 / 0.85 ( 3) link_BETA1-4 : angle 4.75611 / 2.10 ( 9) link_NAG-ASN : bond 0.00218 / 0.11 ( 2) link_NAG-ASN : angle 5.42118 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.047 Fit side-chains REVERT: A 375 ARG cc_start: 0.7480 (mtp180) cc_final: 0.6747 (tpt170) REVERT: A 420 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7672 (ptmt) REVERT: D 576 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7886 (mp0) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.0508 time to fit residues: 2.6531 Evaluate side-chains 46 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 52.701 > 50: distance: 28 - 134: 22.689 distance: 50 - 105: 11.274 distance: 53 - 59: 7.978 distance: 59 - 60: 10.958 distance: 60 - 61: 12.761 distance: 60 - 63: 7.060 distance: 61 - 62: 15.269 distance: 63 - 64: 13.279 distance: 63 - 65: 17.972 distance: 66 - 67: 16.179 distance: 67 - 68: 12.571 distance: 67 - 70: 21.649 distance: 68 - 69: 12.329 distance: 70 - 71: 41.855 distance: 71 - 72: 3.635 distance: 72 - 73: 14.334 distance: 74 - 75: 12.243 distance: 75 - 76: 20.713 distance: 75 - 78: 19.527 distance: 76 - 77: 15.514 distance: 76 - 82: 34.650 distance: 78 - 79: 18.561 distance: 79 - 80: 9.992 distance: 79 - 81: 9.139 distance: 82 - 83: 24.086 distance: 83 - 84: 16.879 distance: 83 - 86: 21.415 distance: 84 - 85: 11.615 distance: 84 - 91: 4.360 distance: 86 - 87: 8.073 distance: 87 - 88: 35.330 distance: 88 - 89: 17.426 distance: 88 - 90: 28.958 distance: 91 - 92: 11.999 distance: 92 - 93: 11.216 distance: 92 - 95: 5.228 distance: 93 - 94: 4.601 distance: 93 - 100: 9.055 distance: 95 - 96: 17.761 distance: 96 - 97: 13.124 distance: 97 - 98: 3.061 distance: 98 - 99: 13.215 distance: 100 - 101: 20.358 distance: 101 - 102: 17.499 distance: 101 - 104: 13.492 distance: 102 - 103: 21.242 distance: 102 - 106: 32.267 distance: 104 - 105: 19.688 distance: 106 - 107: 15.608 distance: 107 - 108: 8.749 distance: 107 - 110: 20.818 distance: 108 - 109: 35.556 distance: 108 - 115: 4.866 distance: 110 - 111: 8.293 distance: 111 - 112: 14.348 distance: 112 - 113: 9.872 distance: 113 - 114: 23.925 distance: 115 - 116: 6.275 distance: 115 - 121: 23.774 distance: 116 - 117: 8.722 distance: 117 - 118: 21.464 distance: 117 - 122: 33.993 distance: 119 - 120: 33.820 distance: 120 - 121: 20.478 distance: 122 - 123: 13.735 distance: 123 - 124: 26.727 distance: 123 - 126: 11.037 distance: 124 - 125: 10.744 distance: 124 - 129: 14.137 distance: 126 - 127: 13.557 distance: 126 - 128: 12.925 distance: 129 - 130: 7.907 distance: 130 - 131: 9.291 distance: 130 - 133: 16.273 distance: 131 - 132: 10.735 distance: 131 - 135: 22.362 distance: 133 - 134: 18.739