Starting phenix.real_space_refine on Fri Aug 22 14:48:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8c_61227/08_2025/9j8c_61227.map" } resolution = 2.9 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= 0.057 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: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2963 2.51 5 N 677 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4418 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4311 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 101 Unusual residues: {' CL': 1, ' NA': 2, 'CLR': 3} Classifications: {'undetermined': 6, 'water': 14} Link IDs: {None: 19} Time building chain proxies: 1.03, per 1000 atoms: 0.23 Number of scatterers: 4418 At special positions: 0 Unit cell: (79.9, 69.7, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 740 8.00 N 677 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 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: 0.35 Conformation dependent library (CDL) restraints added in 146.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.518A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.819A pdb=" N VAL A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.214A pdb=" N TYR A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.751A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.900A pdb=" N TRP A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.973A pdb=" N TYR A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 263 through 283 Proline residue: A 269 - end of helix removed outlier: 4.036A pdb=" N ARG A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.682A pdb=" N GLY A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.907A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.684A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 372 removed outlier: 3.654A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 391 - end of helix removed outlier: 3.841A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.771A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.907A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.730A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.601A pdb=" N MET A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.503A pdb=" N VAL A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.203A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.574A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 3.521A pdb=" N ALA A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 262 hydrogen bonds defined for protein. 771 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: 0.39 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 963 1.33 - 1.45: 1091 1.45 - 1.57: 2441 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4548 Sorted by residual: bond pdb=" C VAL A 261 " pdb=" N VAL A 262 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.28e-02 6.10e+03 2.50e+00 bond pdb=" C GLY A 177 " pdb=" O GLY A 177 " ideal model delta sigma weight residual 1.233 1.215 0.018 1.18e-02 7.18e+03 2.42e+00 bond pdb=" C VAL A 178 " pdb=" O VAL A 178 " ideal model delta sigma weight residual 1.238 1.219 0.019 1.32e-02 5.74e+03 2.01e+00 bond pdb=" CA VAL A 178 " pdb=" CB VAL A 178 " ideal model delta sigma weight residual 1.540 1.525 0.016 1.15e-02 7.56e+03 1.83e+00 bond pdb=" CA GLY A 80 " pdb=" C GLY A 80 " ideal model delta sigma weight residual 1.513 1.529 -0.016 1.23e-02 6.61e+03 1.68e+00 ... (remaining 4543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5998 1.48 - 2.97: 160 2.97 - 4.45: 36 4.45 - 5.93: 20 5.93 - 7.41: 4 Bond angle restraints: 6218 Sorted by residual: angle pdb=" N VAL A 262 " pdb=" CA VAL A 262 " pdb=" C VAL A 262 " ideal model delta sigma weight residual 113.16 105.75 7.41 1.49e+00 4.50e-01 2.48e+01 angle pdb=" N GLY A 177 " pdb=" CA GLY A 177 " pdb=" C GLY A 177 " ideal model delta sigma weight residual 110.90 117.72 -6.82 1.53e+00 4.27e-01 1.99e+01 angle pdb=" C LYS A 260 " pdb=" N VAL A 261 " pdb=" CA VAL A 261 " ideal model delta sigma weight residual 121.97 128.80 -6.83 1.80e+00 3.09e-01 1.44e+01 angle pdb=" N ILE A 496 " pdb=" CA ILE A 496 " pdb=" C ILE A 496 " ideal model delta sigma weight residual 111.81 108.90 2.91 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N ALA A 266 " pdb=" CA ALA A 266 " pdb=" C ALA A 266 " ideal model delta sigma weight residual 114.31 110.08 4.23 1.29e+00 6.01e-01 1.08e+01 ... (remaining 6213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2326 17.05 - 34.11: 282 34.11 - 51.16: 76 51.16 - 68.21: 18 68.21 - 85.27: 3 Dihedral angle restraints: 2705 sinusoidal: 1145 harmonic: 1560 Sorted by residual: dihedral pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual 180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL A 434 " pdb=" C VAL A 434 " pdb=" N GLY A 435 " pdb=" CA GLY A 435 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 621 0.070 - 0.140: 56 0.140 - 0.209: 10 0.209 - 0.279: 4 0.279 - 0.349: 2 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL A 261 " pdb=" CA VAL A 261 " pdb=" CG1 VAL A 261 " pdb=" CG2 VAL A 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C14 CLR A 703 " pdb=" C13 CLR A 703 " pdb=" C15 CLR A 703 " pdb=" C8 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 690 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 261 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C VAL A 261 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 261 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 262 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 542 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 543 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 176 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA A 176 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA A 176 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 177 " -0.011 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1154 2.80 - 3.32: 3949 3.32 - 3.85: 7177 3.85 - 4.37: 8360 4.37 - 4.90: 14815 Nonbonded interactions: 35455 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb=" O HOH A 801 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN A 68 " pdb="NA NA A 706 " model vdw 2.297 2.470 nonbonded pdb=" O ALA A 63 " pdb="NA NA A 706 " model vdw 2.311 2.470 nonbonded pdb=" OG SER A 486 " pdb=" O HOH A 802 " model vdw 2.318 3.040 nonbonded pdb=" N ASP A 599 " pdb=" OD1 ASP A 599 " model vdw 2.340 3.120 ... (remaining 35450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.140 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:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.049 4549 Z= 0.156 Angle : 0.671 7.413 6220 Z= 0.364 Chirality : 0.050 0.349 693 Planarity : 0.004 0.047 746 Dihedral : 15.960 85.267 1716 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % 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 aren not related in a simple way. whole: 1.43 (0.38), residues: 538 helix: 1.92 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 500 TYR 0.015 0.001 TYR A 74 PHE 0.011 0.001 PHE A 100 TRP 0.009 0.001 TRP A 554 HIS 0.006 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4548) covalent geometry : angle 0.67053 ( 6218) SS BOND : bond 0.00048 ( 1) SS BOND : angle 1.11553 ( 2) hydrogen bonds : bond 0.17698 ( 262) hydrogen bonds : angle 5.37477 ( 771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.155 Fit side-chains REVERT: A 253 ARG cc_start: 0.5691 (ptt180) cc_final: 0.5232 (mtp180) REVERT: A 299 ASP cc_start: 0.8050 (t0) cc_final: 0.7367 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4699 time to fit residues: 27.8155 Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.089881 restraints weight = 5140.964| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.54 r_work: 0.2712 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4549 Z= 0.131 Angle : 0.521 5.429 6220 Z= 0.271 Chirality : 0.039 0.118 693 Planarity : 0.005 0.040 746 Dihedral : 7.268 59.396 790 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.18 % Allowed : 22.05 % Favored : 75.76 % 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 aren not related in a simple way. whole: 1.72 (0.38), residues: 538 helix: 2.07 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -1.18 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 580 TYR 0.020 0.001 TYR A 74 PHE 0.016 0.001 PHE A 84 TRP 0.010 0.001 TRP A 215 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4548) covalent geometry : angle 0.52045 ( 6218) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.99824 ( 2) hydrogen bonds : bond 0.06282 ( 262) hydrogen bonds : angle 4.04595 ( 771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.105 Fit side-chains REVERT: A 74 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8440 (p90) REVERT: A 253 ARG cc_start: 0.5694 (ptt180) cc_final: 0.5324 (mtp180) REVERT: A 284 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 299 ASP cc_start: 0.8267 (t0) cc_final: 0.7540 (p0) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.4989 time to fit residues: 29.0065 Evaluate side-chains 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 597 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.115313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.088409 restraints weight = 5079.570| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.55 r_work: 0.2684 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4549 Z= 0.135 Angle : 0.514 5.378 6220 Z= 0.268 Chirality : 0.039 0.119 693 Planarity : 0.004 0.038 746 Dihedral : 7.364 61.058 790 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.40 % Allowed : 21.62 % Favored : 75.98 % 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 aren not related in a simple way. whole: 1.80 (0.38), residues: 538 helix: 2.17 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.24 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 580 TYR 0.021 0.001 TYR A 74 PHE 0.017 0.001 PHE A 84 TRP 0.012 0.001 TRP A 215 HIS 0.005 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4548) covalent geometry : angle 0.51376 ( 6218) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.96199 ( 2) hydrogen bonds : bond 0.06167 ( 262) hydrogen bonds : angle 3.91312 ( 771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.169 Fit side-chains REVERT: A 57 LEU cc_start: 0.6777 (mt) cc_final: 0.6548 (mt) REVERT: A 74 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8416 (p90) REVERT: A 253 ARG cc_start: 0.5778 (ptt180) cc_final: 0.5517 (mtp180) REVERT: A 299 ASP cc_start: 0.8225 (t0) cc_final: 0.7537 (p0) REVERT: A 494 MET cc_start: 0.9185 (mmt) cc_final: 0.8966 (mmp) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 0.5387 time to fit residues: 31.3445 Evaluate side-chains 50 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.115308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.088234 restraints weight = 5137.409| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.57 r_work: 0.2684 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4549 Z= 0.130 Angle : 0.505 5.392 6220 Z= 0.262 Chirality : 0.039 0.119 693 Planarity : 0.004 0.038 746 Dihedral : 7.375 61.302 790 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.62 % Allowed : 22.27 % Favored : 75.11 % 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 aren not related in a simple way. whole: 1.85 (0.38), residues: 538 helix: 2.24 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.29 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.021 0.001 TYR A 74 PHE 0.017 0.001 PHE A 84 TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4548) covalent geometry : angle 0.50413 ( 6218) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.26030 ( 2) hydrogen bonds : bond 0.05928 ( 262) hydrogen bonds : angle 3.85862 ( 771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.120 Fit side-chains REVERT: A 57 LEU cc_start: 0.6741 (mt) cc_final: 0.6461 (mt) REVERT: A 74 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8398 (p90) REVERT: A 284 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: A 299 ASP cc_start: 0.8191 (t0) cc_final: 0.7499 (p0) outliers start: 12 outliers final: 7 residues processed: 56 average time/residue: 0.5652 time to fit residues: 32.7272 Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 61.0493 > 50: distance: 20 - 45: 10.744 distance: 35 - 40: 14.887 distance: 40 - 41: 35.658 distance: 41 - 42: 16.263 distance: 41 - 44: 29.944 distance: 42 - 43: 6.378 distance: 42 - 46: 8.238 distance: 44 - 45: 24.223 distance: 46 - 47: 18.368 distance: 47 - 48: 19.190 distance: 47 - 50: 29.707 distance: 48 - 49: 19.563 distance: 48 - 51: 8.131 distance: 51 - 52: 37.973 distance: 52 - 53: 12.234 distance: 53 - 54: 20.804 distance: 53 - 55: 5.839 distance: 55 - 56: 7.216 distance: 56 - 57: 9.617 distance: 57 - 58: 10.964 distance: 57 - 62: 17.142 distance: 59 - 60: 5.105 distance: 59 - 61: 13.926 distance: 62 - 63: 7.744 distance: 63 - 64: 6.141 distance: 63 - 66: 8.354 distance: 64 - 65: 6.672 distance: 66 - 67: 4.298 distance: 67 - 68: 10.365 distance: 67 - 69: 4.031 distance: 70 - 71: 7.445 distance: 71 - 72: 14.988 distance: 71 - 74: 3.707 distance: 72 - 73: 11.252 distance: 72 - 81: 18.248 distance: 74 - 75: 6.229 distance: 76 - 77: 4.111 distance: 78 - 79: 3.659 distance: 78 - 80: 4.194 distance: 81 - 82: 7.165 distance: 82 - 83: 24.956 distance: 82 - 85: 10.697 distance: 83 - 84: 28.423 distance: 83 - 88: 16.869 distance: 85 - 86: 11.485 distance: 85 - 87: 20.298 distance: 88 - 89: 13.504 distance: 89 - 90: 22.380 distance: 89 - 92: 13.373 distance: 90 - 91: 33.172 distance: 90 - 94: 15.138 distance: 91 - 115: 24.670 distance: 92 - 93: 52.318 distance: 94 - 95: 11.748 distance: 94 - 100: 38.346 distance: 95 - 96: 23.400 distance: 95 - 98: 30.885 distance: 96 - 97: 21.043 distance: 96 - 101: 11.039 distance: 97 - 124: 19.876 distance: 98 - 99: 11.321 distance: 99 - 100: 44.010 distance: 101 - 102: 17.241 distance: 102 - 103: 7.431 distance: 102 - 105: 22.440 distance: 103 - 104: 30.550 distance: 103 - 107: 10.362 distance: 104 - 131: 34.766 distance: 105 - 106: 21.680