Starting phenix.real_space_refine on Tue Feb 3 14:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.map" model { file = "/net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j04_61048/02_2026/9j04_61048.cif" } resolution = 3.15 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= 0.013 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 C 2450 2.51 5 N 639 2.21 5 O 662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3782 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3764 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 26, 'TRANS': 461} Chain breaks: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'L8P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.28 Number of scatterers: 3782 At special positions: 0 Unit cell: (102, 58.65, 76.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 1 15.00 O 662 8.00 N 639 7.00 C 2450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 146.4 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 67.6% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 14 through 26 removed outlier: 4.806A pdb=" N THR A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.585A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.700A pdb=" N LEU A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 211 removed outlier: 3.621A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.640A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.765A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.604A pdb=" N HIS A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.050A pdb=" N THR A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 332 through 357 removed outlier: 3.905A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.382A pdb=" N VAL A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.567A pdb=" N ILE A 389 " --> pdb=" O GLY A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 424 through 449 removed outlier: 3.979A pdb=" N LEU A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.794A pdb=" N GLY A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Proline residue: A 473 - end of helix removed outlier: 3.712A pdb=" N SER A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.669A pdb=" N GLU A 480 " --> pdb=" O MET A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.633A pdb=" N VAL A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.824A pdb=" N LEU A 504 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.714A pdb=" N HIS A 48 " --> pdb=" O ILE A 110 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 546 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: 0.52 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 580 1.32 - 1.45: 1128 1.45 - 1.59: 2114 1.59 - 1.72: 0 1.72 - 1.86: 48 Bond restraints: 3870 Sorted by residual: bond pdb=" C5 L8P A 601 " pdb=" C6 L8P A 601 " ideal model delta sigma weight residual 1.348 1.490 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 L8P A 601 " pdb=" N3 L8P A 601 " ideal model delta sigma weight residual 1.349 1.486 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C4 L8P A 601 " pdb=" N3 L8P A 601 " ideal model delta sigma weight residual 1.316 1.448 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4 L8P A 601 " pdb=" N4 L8P A 601 " ideal model delta sigma weight residual 1.343 1.451 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C6 L8P A 601 " pdb=" N1 L8P A 601 " ideal model delta sigma weight residual 1.349 1.455 -0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 3865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 5165 1.89 - 3.78: 84 3.78 - 5.66: 16 5.66 - 7.55: 1 7.55 - 9.44: 2 Bond angle restraints: 5268 Sorted by residual: angle pdb=" N ILE A 373 " pdb=" CA ILE A 373 " pdb=" C ILE A 373 " ideal model delta sigma weight residual 112.96 108.38 4.58 1.00e+00 1.00e+00 2.09e+01 angle pdb=" C VAL A 127 " pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" O4' L8P A 601 " pdb=" C4' L8P A 601 " pdb=" P L8P A 601 " ideal model delta sigma weight residual 116.17 106.73 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.62 109.22 2.40 7.90e-01 1.60e+00 9.22e+00 angle pdb=" C4' L8P A 601 " pdb=" P L8P A 601 " pdb=" OP1 L8P A 601 " ideal model delta sigma weight residual 101.44 109.44 -8.00 3.00e+00 1.11e-01 7.11e+00 ... (remaining 5263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 1993 14.58 - 29.15: 232 29.15 - 43.73: 45 43.73 - 58.31: 8 58.31 - 72.88: 6 Dihedral angle restraints: 2284 sinusoidal: 880 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TYR A 354 " pdb=" C TYR A 354 " pdb=" N GLY A 355 " pdb=" CA GLY A 355 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 466 " pdb=" C ARG A 466 " pdb=" N VAL A 467 " pdb=" CA VAL A 467 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.09e+00 ... (remaining 2281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 316 0.027 - 0.054: 187 0.054 - 0.081: 69 0.081 - 0.109: 34 0.109 - 0.136: 8 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C2' L8P A 601 " pdb=" C1' L8P A 601 " pdb=" C3' L8P A 601 " pdb=" O4' L8P A 601 " both_signs ideal model delta sigma weight residual False -2.39 -2.52 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ASP A 359 " pdb=" N ASP A 359 " pdb=" C ASP A 359 " pdb=" CB ASP A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 611 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A 27 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 244 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 245 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 449 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 450 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.021 5.00e-02 4.00e+02 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1343 2.86 - 3.37: 3566 3.37 - 3.88: 5762 3.88 - 4.39: 6611 4.39 - 4.90: 11233 Nonbonded interactions: 28515 Sorted by model distance: nonbonded pdb=" O SER A 265 " pdb=" OG SER A 265 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 255 " pdb=" OG SER A 255 " model vdw 2.351 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OD2 ASP A 107 " model vdw 2.352 3.120 nonbonded pdb=" NH2 ARG A 131 " pdb=" OE1 GLU A 480 " model vdw 2.391 3.120 nonbonded pdb=" NE ARG A 69 " pdb=" O GLY A 73 " model vdw 2.432 3.120 ... (remaining 28510 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.730 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.006 0.142 3870 Z= 0.292 Angle : 0.655 9.438 5268 Z= 0.351 Chirality : 0.042 0.136 614 Planarity : 0.005 0.054 659 Dihedral : 13.043 72.883 1380 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -3.44 (0.34), residues: 480 helix: -1.91 (0.25), residues: 323 sheet: None (None), residues: 0 loop : -2.77 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.014 0.002 TYR A 264 PHE 0.017 0.001 PHE A 438 TRP 0.014 0.001 TRP A 346 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 3870) covalent geometry : angle 0.65510 ( 5268) hydrogen bonds : bond 0.14709 ( 184) hydrogen bonds : angle 5.22993 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.142 Fit side-chains REVERT: A 107 ASP cc_start: 0.7928 (m-30) cc_final: 0.7492 (m-30) REVERT: A 142 MET cc_start: 0.8189 (mmt) cc_final: 0.6677 (mmt) REVERT: A 369 LEU cc_start: 0.8499 (tp) cc_final: 0.8203 (tp) REVERT: A 455 GLN cc_start: 0.8498 (mm110) cc_final: 0.7443 (pm20) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0840 time to fit residues: 9.3258 Evaluate side-chains 67 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 398 GLN A 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101941 restraints weight = 4472.637| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.87 r_work: 0.3160 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3870 Z= 0.138 Angle : 0.599 8.686 5268 Z= 0.299 Chirality : 0.042 0.218 614 Planarity : 0.005 0.045 659 Dihedral : 5.060 57.550 535 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.98 % Allowed : 11.36 % Favored : 86.67 % 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: -1.90 (0.38), residues: 480 helix: -0.75 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -2.15 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.011 0.001 TYR A 169 PHE 0.013 0.001 PHE A 351 TRP 0.015 0.001 TRP A 346 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3870) covalent geometry : angle 0.59858 ( 5268) hydrogen bonds : bond 0.04952 ( 184) hydrogen bonds : angle 4.07621 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.172 Fit side-chains REVERT: A 286 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8928 (tpp80) REVERT: A 336 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7352 (ptp90) REVERT: A 369 LEU cc_start: 0.8398 (tp) cc_final: 0.8165 (tp) REVERT: A 417 GLN cc_start: 0.8215 (mt0) cc_final: 0.7814 (mp10) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.0833 time to fit residues: 7.3646 Evaluate side-chains 79 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 518 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2469 > 50: distance: 22 - 33: 3.017 distance: 89 - 106: 5.298 distance: 93 - 110: 14.011 distance: 102 - 106: 3.362 distance: 103 - 123: 6.566 distance: 106 - 107: 6.936 distance: 107 - 108: 10.240 distance: 108 - 109: 10.667 distance: 108 - 110: 14.467 distance: 109 - 131: 8.053 distance: 110 - 111: 8.275 distance: 111 - 112: 6.406 distance: 111 - 114: 4.471 distance: 112 - 113: 10.128 distance: 112 - 118: 5.347 distance: 114 - 115: 3.942 distance: 115 - 116: 12.189 distance: 116 - 117: 15.134 distance: 119 - 120: 10.870 distance: 119 - 122: 7.602 distance: 120 - 121: 11.005 distance: 120 - 123: 3.686 distance: 121 - 140: 33.029 distance: 123 - 124: 5.905 distance: 124 - 125: 4.002 distance: 124 - 127: 7.115 distance: 125 - 126: 11.105 distance: 125 - 131: 8.355 distance: 126 - 148: 22.444 distance: 127 - 128: 8.647 distance: 128 - 129: 12.164 distance: 128 - 130: 5.897 distance: 131 - 132: 6.202 distance: 132 - 133: 3.278 distance: 132 - 135: 6.478 distance: 133 - 134: 11.300 distance: 133 - 136: 10.020 distance: 136 - 137: 20.292 distance: 137 - 138: 10.075 distance: 138 - 139: 7.903 distance: 138 - 140: 7.336 distance: 139 - 162: 20.520 distance: 140 - 141: 8.549 distance: 141 - 142: 9.609 distance: 141 - 144: 11.373 distance: 142 - 143: 12.183 distance: 142 - 148: 13.523 distance: 143 - 170: 8.869 distance: 144 - 145: 12.591 distance: 144 - 146: 10.402 distance: 145 - 147: 8.289 distance: 148 - 149: 24.852 distance: 149 - 150: 22.050 distance: 149 - 152: 14.302 distance: 150 - 151: 25.169 distance: 150 - 154: 25.535 distance: 152 - 153: 3.087 distance: 154 - 155: 14.559 distance: 155 - 156: 8.191 distance: 155 - 158: 9.344 distance: 156 - 157: 4.721 distance: 157 - 182: 5.871 distance: 158 - 159: 23.490 distance: 159 - 160: 53.032 distance: 159 - 161: 22.188 distance: 162 - 163: 5.918 distance: 163 - 166: 6.252 distance: 164 - 165: 7.149 distance: 164 - 170: 6.315 distance: 165 - 188: 9.634 distance: 166 - 167: 6.688 distance: 167 - 168: 9.344 distance: 167 - 169: 7.474