Starting phenix.real_space_refine on Wed Jul 1 22:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i52_4410/07_2026/6i52_4410.map" } resolution = 4.7 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= 0.002 sd= 0.012 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 20 5.49 5 S 16 5.16 5 C 2377 2.51 5 N 635 2.21 5 O 808 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3856 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 966 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1041 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1449 Classifications: {'peptide': 178} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 171} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 0.78, per 1000 atoms: 0.20 Number of scatterers: 3856 At special positions: 0 Unit cell: (82.68, 65.72, 107.06, 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 16 16.00 P 20 15.00 O 808 8.00 N 635 7.00 C 2377 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 130.8 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 828 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 22.9% alpha, 24.1% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.969A pdb=" N ILE A 13 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 14 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.682A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.704A pdb=" N LEU B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.590A pdb=" N GLN C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 450 through 455' Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.646A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 557 Processing helix chain 'C' and resid 561 through 571 Processing helix chain 'C' and resid 604 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.827A pdb=" N ARG A 78 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 89 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.877A pdb=" N ILE A 37 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.712A pdb=" N SER B 61 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.131A pdb=" N GLY B 73 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 134 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 468 through 476 removed outlier: 4.815A pdb=" N ILE C 473 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 526 " --> pdb=" O ILE C 473 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLN C 531 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N TYR C 594 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP C 533 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 596 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR C 535 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN C 598 " --> pdb=" O THR C 535 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C 591 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 584 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 580 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG C 578 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 599 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 576 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 482 through 484 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 497 108 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.48 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1129 1.34 - 1.45: 627 1.45 - 1.57: 2136 1.57 - 1.69: 39 1.69 - 1.81: 23 Bond restraints: 3954 Sorted by residual: bond pdb=" C3' DT D 11 " pdb=" C2' DT D 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 bond pdb=" C3' DT D 13 " pdb=" C2' DT D 13 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.26e+00 bond pdb=" C1' DT D 13 " pdb=" N1 DT D 13 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.81e+00 bond pdb=" C1' DT D 21 " pdb=" N1 DT D 21 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C1' DT D 18 " pdb=" N1 DT D 18 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.51e+00 ... (remaining 3949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5155 1.39 - 2.78: 239 2.78 - 4.17: 27 4.17 - 5.56: 6 5.56 - 6.95: 2 Bond angle restraints: 5429 Sorted by residual: angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 26 " pdb=" C4 DT D 26 " pdb=" O4 DT D 26 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 23 " pdb=" C4 DT D 23 " pdb=" O4 DT D 23 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT D 27 " pdb=" C4 DT D 27 " pdb=" O4 DT D 27 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 2228 29.30 - 58.61: 90 58.61 - 87.91: 15 87.91 - 117.21: 2 117.21 - 146.51: 3 Dihedral angle restraints: 2338 sinusoidal: 1070 harmonic: 1268 Sorted by residual: dihedral pdb=" CA GLU C 462 " pdb=" C GLU C 462 " pdb=" N LYS C 463 " pdb=" CA LYS C 463 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 466 " pdb=" C PHE C 466 " pdb=" N PHE C 467 " pdb=" CA PHE C 467 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT D 11 " pdb=" C3' DT D 11 " pdb=" O3' DT D 11 " pdb=" P DT D 12 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 2335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 359 0.027 - 0.054: 154 0.054 - 0.081: 51 0.081 - 0.109: 38 0.109 - 0.136: 16 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA THR B 79 " pdb=" N THR B 79 " pdb=" C THR B 79 " pdb=" CB THR B 79 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" C3' DT D 11 " pdb=" C4' DT D 11 " pdb=" O3' DT D 11 " pdb=" C2' DT D 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 615 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 79 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C THR B 79 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 79 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP B 80 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 30 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 31 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 118 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 119 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.019 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1101 2.82 - 3.34: 3351 3.34 - 3.86: 6120 3.86 - 4.38: 6724 4.38 - 4.90: 11453 Nonbonded interactions: 28749 Sorted by model distance: nonbonded pdb=" OD2 ASP A 9 " pdb=" OG1 THR A 11 " model vdw 2.303 3.040 nonbonded pdb=" ND1 HIS B 68 " pdb=" O GLY B 138 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP C 500 " pdb=" N GLY C 501 " model vdw 2.330 3.120 nonbonded pdb=" OG SER C 474 " pdb=" O SER C 524 " model vdw 2.339 3.040 nonbonded pdb=" O VAL B 163 " pdb=" ND1 HIS B 166 " model vdw 2.361 3.120 ... (remaining 28744 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: 0.130 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.110 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 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 0.050 3954 Z= 0.262 Angle : 0.641 6.949 5429 Z= 0.514 Chirality : 0.042 0.136 618 Planarity : 0.004 0.047 639 Dihedral : 16.564 146.514 1510 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Rotamer: Outliers : 5.70 % Allowed : 9.84 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -4.07 (0.31), residues: 424 helix: -3.47 (0.33), residues: 95 sheet: -1.85 (0.49), residues: 77 loop : -2.75 (0.30), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 591 TYR 0.010 0.001 TYR B 151 PHE 0.016 0.001 PHE C 467 TRP 0.004 0.001 TRP C 533 HIS 0.002 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.26 ( 3954) covalent geometry : angle 0.64085 / 0.51 ( 5429) hydrogen bonds : bond 0.15029 / 10.30 ( 108) hydrogen bonds : angle 12.38356 / 8.43 ( 294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.6037 (OUTLIER) cc_final: 0.5038 (mp10) REVERT: A 53 MET cc_start: 0.6572 (mtm) cc_final: 0.6343 (mpp) REVERT: A 75 PHE cc_start: 0.7684 (t80) cc_final: 0.7453 (t80) REVERT: B 160 PHE cc_start: 0.6461 (p90) cc_final: 0.6220 (p90) REVERT: B 167 HIS cc_start: 0.8149 (m-70) cc_final: 0.7539 (t-170) REVERT: C 478 VAL cc_start: 0.4301 (OUTLIER) cc_final: 0.3902 (t) REVERT: C 479 ASP cc_start: 0.8308 (m-30) cc_final: 0.7717 (p0) REVERT: C 531 GLN cc_start: 0.7691 (pt0) cc_final: 0.7128 (tm-30) outliers start: 22 outliers final: 6 residues processed: 129 average time/residue: 0.0666 time to fit residues: 10.4438 Evaluate side-chains 54 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 35 GLN A 80 ASN B 63 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.083969 restraints weight = 28829.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.085500 restraints weight = 23920.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.086633 restraints weight = 20830.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.087549 restraints weight = 18703.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.088271 restraints weight = 17157.177| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3954 Z= 0.166 Angle : 0.733 8.401 5429 Z= 0.399 Chirality : 0.048 0.225 618 Planarity : 0.007 0.078 639 Dihedral : 19.517 146.906 657 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.02 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % 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: -3.08 (0.34), residues: 424 helix: -1.38 (0.49), residues: 89 sheet: -1.18 (0.55), residues: 77 loop : -2.71 (0.30), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 593 TYR 0.023 0.002 TYR B 151 PHE 0.022 0.002 PHE A 75 TRP 0.035 0.003 TRP B 101 HIS 0.007 0.002 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 3954) covalent geometry : angle 0.73258 / 0.40 ( 5429) hydrogen bonds : bond 0.03942 / 2.78 ( 108) hydrogen bonds : angle 8.83940 / 5.99 ( 294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.6989 (t80) cc_final: 0.5666 (t80) REVERT: B 135 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8259 (mmtt) REVERT: B 160 PHE cc_start: 0.6965 (p90) cc_final: 0.6758 (p90) REVERT: B 167 HIS cc_start: 0.8238 (m-70) cc_final: 0.8020 (m-70) REVERT: C 532 LEU cc_start: 0.6291 (tp) cc_final: 0.6038 (mm) REVERT: C 536 LEU cc_start: 0.9049 (mp) cc_final: 0.8689 (mp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0487 time to fit residues: 4.2528 Evaluate side-chains 40 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.759 > 50: distance: 95 - 101: 24.918 distance: 101 - 102: 10.146 distance: 102 - 103: 12.069 distance: 102 - 105: 13.404 distance: 103 - 104: 13.847 distance: 103 - 110: 28.398 distance: 105 - 106: 32.783 distance: 106 - 107: 28.836 distance: 107 - 108: 18.302 distance: 107 - 109: 14.441 distance: 110 - 111: 9.346 distance: 111 - 112: 29.282 distance: 111 - 114: 8.800 distance: 112 - 113: 11.744 distance: 112 - 122: 28.686 distance: 114 - 115: 8.592 distance: 115 - 116: 30.364 distance: 115 - 117: 10.552 distance: 116 - 118: 12.215 distance: 117 - 119: 26.723 distance: 118 - 120: 31.799 distance: 119 - 120: 22.482 distance: 120 - 121: 6.001 distance: 122 - 123: 9.985 distance: 123 - 124: 8.046 distance: 123 - 126: 33.254 distance: 124 - 127: 40.576 distance: 127 - 128: 14.834 distance: 128 - 129: 23.690 distance: 128 - 131: 17.468 distance: 129 - 130: 20.211 distance: 129 - 134: 18.997 distance: 131 - 132: 43.235 distance: 131 - 133: 17.192 distance: 134 - 135: 29.660 distance: 135 - 136: 23.404 distance: 135 - 138: 24.472 distance: 136 - 137: 23.227 distance: 136 - 142: 44.572 distance: 138 - 139: 15.656 distance: 138 - 140: 25.411 distance: 139 - 141: 14.583 distance: 142 - 143: 38.284 distance: 143 - 144: 16.480 distance: 143 - 146: 38.455 distance: 144 - 145: 25.666 distance: 144 - 151: 24.285 distance: 146 - 147: 21.126 distance: 147 - 148: 22.120 distance: 148 - 149: 16.654 distance: 149 - 150: 30.569 distance: 151 - 152: 21.011 distance: 151 - 157: 45.151 distance: 152 - 155: 40.378 distance: 153 - 154: 4.176 distance: 153 - 158: 18.995 distance: 155 - 156: 26.247 distance: 156 - 157: 49.552 distance: 158 - 159: 40.597 distance: 159 - 160: 15.252 distance: 159 - 162: 11.599 distance: 160 - 161: 10.912 distance: 160 - 166: 7.552 distance: 162 - 163: 19.885 distance: 162 - 164: 31.784 distance: 166 - 167: 14.069 distance: 167 - 170: 8.918 distance: 168 - 169: 16.686 distance: 168 - 174: 10.555 distance: 170 - 171: 8.460 distance: 171 - 172: 12.123 distance: 171 - 173: 10.497 distance: 174 - 175: 24.526 distance: 175 - 176: 12.122 distance: 175 - 178: 21.746 distance: 176 - 177: 27.835 distance: 176 - 180: 11.375 distance: 178 - 179: 34.730