Starting phenix.real_space_refine on Fri Aug 22 19:22:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1k_40970/08_2025/8t1k_40970.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.141 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 Fe 2 7.16 5 Zn 1 6.06 5 S 42 5.16 5 C 4460 2.51 5 N 1202 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s 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: 6973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1} Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'H4B': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 234 SG CYS A 326 36.136 27.320 47.401 1.00 0.00 S ATOM 274 SG CYS A 331 36.502 30.069 50.826 1.00 0.00 S ATOM 3648 SG CYS B 326 33.713 27.338 51.424 1.00 0.00 S ATOM 3688 SG CYS B 331 33.825 30.349 48.205 1.00 0.00 S ATOM 965 SG CYS A 415 29.189 41.684 34.489 1.00 0.00 S ATOM 4379 SG CYS B 415 43.340 39.579 64.879 1.00 0.00 S Time building chain proxies: 2.15, per 1000 atoms: 0.31 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.784, 82.992, 101.232, 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) Zn 1 29.99 Fe 2 26.01 S 42 16.00 O 1266 8.00 N 1202 7.00 C 4460 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 404.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 326 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 350 through 369 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'A' and resid 624 through 644 Processing helix chain 'A' and resid 650 through 669 removed outlier: 3.586A pdb=" N THR A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 684 through 693 Proline residue: A 689 - end of helix removed outlier: 3.647A pdb=" N HIS A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 350 through 369 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 498 through 507 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 624 through 644 Processing helix chain 'B' and resid 650 through 669 Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 684 through 692 Proline residue: B 689 - end of helix removed outlier: 3.614A pdb=" N HIS B 692 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 428 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 486 Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589 removed outlier: 6.499A pdb=" N TYR A 588 " --> pdb=" O VAL A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 428 Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB5, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AB6, first strand: chain 'B' and resid 577 through 579 Processing sheet with id=AB7, first strand: chain 'B' and resid 588 through 589 removed outlier: 6.190A pdb=" N TYR B 588 " --> pdb=" O VAL B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 295 hydrogen bonds defined for protein. 738 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: 1.12 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 2195 1.35 - 1.55: 4911 1.55 - 1.76: 4 1.76 - 1.96: 65 1.96 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.18e-02 7.18e+03 6.35e+01 bond pdb=" CA TYR B 588 " pdb=" C TYR B 588 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.24e-02 6.50e+03 6.31e+01 bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.393 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " ideal model delta sigma weight residual 1.544 1.394 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C3C HEM B1503 " pdb=" CAC HEM B1503 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 9683 5.39 - 10.77: 83 10.77 - 16.16: 2 16.16 - 21.55: 0 21.55 - 26.93: 2 Bond angle restraints: 9770 Sorted by residual: angle pdb=" CA TYR B 588 " pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 120.80 111.77 9.03 1.11e+00 8.12e-01 6.62e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.36 119.12 -7.76 1.09e+00 8.42e-01 5.07e+01 angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.06 -7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.57 7.60 1.26e+00 6.30e-01 3.64e+01 angle pdb=" N ASN B 712 " pdb=" CA ASN B 712 " pdb=" C ASN B 712 " ideal model delta sigma weight residual 113.17 105.62 7.55 1.26e+00 6.30e-01 3.59e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 4086 21.63 - 43.27: 99 43.27 - 64.90: 26 64.90 - 86.54: 11 86.54 - 108.17: 8 Dihedral angle restraints: 4230 sinusoidal: 1778 harmonic: 2452 Sorted by residual: dihedral pdb=" C2B HEM A1504 " pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " pdb=" CBB HEM A1504 " ideal model delta sinusoidal sigma weight residual -180.00 -106.49 -73.51 2 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" C2B HEM B1503 " pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " pdb=" CBB HEM B1503 " ideal model delta sinusoidal sigma weight residual -180.00 -117.70 -62.30 2 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA TYR A 588 " pdb=" C TYR A 588 " pdb=" N MET A 589 " pdb=" CA MET A 589 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 709 0.076 - 0.152: 258 0.152 - 0.228: 40 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA ASP A 471 " pdb=" N ASP A 471 " pdb=" C ASP A 471 " pdb=" CB ASP A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA VAL A 474 " pdb=" N VAL A 474 " pdb=" C VAL A 474 " pdb=" CB VAL A 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ASP B 471 " pdb=" N ASP B 471 " pdb=" C ASP B 471 " pdb=" CB ASP B 471 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " -0.016 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C2A HEM A1504 " -0.038 2.00e-02 2.50e+03 pdb=" C3A HEM A1504 " -0.104 2.00e-02 2.50e+03 pdb=" C4A HEM A1504 " -0.015 2.00e-02 2.50e+03 pdb=" CAA HEM A1504 " 0.251 2.00e-02 2.50e+03 pdb=" CHA HEM A1504 " -0.100 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.173 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " -0.161 2.00e-02 2.50e+03 pdb=" NA HEM A1504 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM B1503 " -0.137 2.00e-02 2.50e+03 1.08e-01 2.62e+02 pdb=" C1D HEM B1503 " -0.147 2.00e-02 2.50e+03 pdb=" C2D HEM B1503 " -0.080 2.00e-02 2.50e+03 pdb=" C3D HEM B1503 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM B1503 " -0.002 2.00e-02 2.50e+03 pdb=" CAD HEM B1503 " -0.003 2.00e-02 2.50e+03 pdb=" CHA HEM B1503 " 0.145 2.00e-02 2.50e+03 pdb=" CHD HEM B1503 " 0.179 2.00e-02 2.50e+03 pdb=" CMD HEM B1503 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1504 " -0.164 2.00e-02 2.50e+03 1.01e-01 2.27e+02 pdb=" C1B HEM A1504 " -0.019 2.00e-02 2.50e+03 pdb=" C2B HEM A1504 " 0.013 2.00e-02 2.50e+03 pdb=" C3B HEM A1504 " 0.002 2.00e-02 2.50e+03 pdb=" C4B HEM A1504 " -0.071 2.00e-02 2.50e+03 pdb=" CAB HEM A1504 " 0.092 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.181 2.00e-02 2.50e+03 pdb=" CHC HEM A1504 " 0.073 2.00e-02 2.50e+03 pdb=" CMB HEM A1504 " -0.108 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2278 2.86 - 3.37: 6431 3.37 - 3.88: 11891 3.88 - 4.39: 14786 4.39 - 4.90: 23441 Nonbonded interactions: 58827 Sorted by model distance: nonbonded pdb=" N TYR B 588 " pdb=" O TYR B 588 " model vdw 2.350 2.496 nonbonded pdb=" NZ LYS B 359 " pdb=" OD2 ASP B 363 " model vdw 2.434 3.120 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.469 3.120 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.493 3.120 nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 ... (remaining 58822 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 298 through 716 or resid 1502 through 1504)) selection = chain 'B' } 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: 2.500 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.015 0.461 7186 Z= 0.730 Angle : 1.488 26.935 9776 Z= 0.979 Chirality : 0.074 0.380 1014 Planarity : 0.009 0.126 1240 Dihedral : 12.821 108.170 2646 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.55 % 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: 0.05 (0.26), residues: 834 helix: -0.17 (0.26), residues: 296 sheet: 0.10 (0.54), residues: 76 loop : 0.34 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 414 TYR 0.100 0.014 TYR B 604 PHE 0.035 0.003 PHE B 554 TRP 0.058 0.006 TRP A 676 HIS 0.004 0.000 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.01198 ( 7180) covalent geometry : angle 1.45571 ( 9770) hydrogen bonds : bond 0.21969 ( 295) hydrogen bonds : angle 7.13842 ( 738) metal coordination : bond 0.26199 ( 4) metal coordination : angle 12.44490 ( 6) Misc. bond : bond 0.33198 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1217 time to fit residues: 21.2491 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 642 GLN B 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.111010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.089318 restraints weight = 7821.554| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.42 r_work: 0.2649 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7186 Z= 0.135 Angle : 0.608 15.212 9776 Z= 0.297 Chirality : 0.043 0.135 1014 Planarity : 0.004 0.035 1240 Dihedral : 11.207 94.713 962 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.33 % Allowed : 5.98 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.31 (0.28), residues: 834 helix: 1.58 (0.31), residues: 298 sheet: 0.01 (0.58), residues: 76 loop : 0.70 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 667 TYR 0.012 0.001 TYR B 366 PHE 0.018 0.002 PHE A 355 TRP 0.009 0.001 TRP A 625 HIS 0.005 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7180) covalent geometry : angle 0.60202 ( 9770) hydrogen bonds : bond 0.04679 ( 295) hydrogen bonds : angle 4.66187 ( 738) metal coordination : bond 0.00559 ( 4) metal coordination : angle 3.59021 ( 6) Misc. bond : bond 0.00928 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.275 Fit side-chains REVERT: A 385 ASN cc_start: 0.8196 (t0) cc_final: 0.7711 (m-40) REVERT: A 645 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7791 (mmmt) REVERT: B 573 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8160 (tp30) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.0983 time to fit residues: 11.2491 Evaluate side-chains 73 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.0040 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 507 GLN B 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.109704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.088469 restraints weight = 7783.795| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.39 r_work: 0.2644 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7186 Z= 0.133 Angle : 0.579 16.061 9776 Z= 0.274 Chirality : 0.042 0.136 1014 Planarity : 0.004 0.035 1240 Dihedral : 11.004 93.216 962 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.33 % Allowed : 7.05 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.28 (0.29), residues: 834 helix: 1.68 (0.31), residues: 298 sheet: 0.24 (0.53), residues: 96 loop : 0.55 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 667 TYR 0.011 0.001 TYR B 366 PHE 0.017 0.002 PHE A 355 TRP 0.008 0.001 TRP A 625 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7180) covalent geometry : angle 0.57367 ( 9770) hydrogen bonds : bond 0.04481 ( 295) hydrogen bonds : angle 4.45635 ( 738) metal coordination : bond 0.00372 ( 4) metal coordination : angle 3.30385 ( 6) Misc. bond : bond 0.01401 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.296 Fit side-chains REVERT: A 385 ASN cc_start: 0.8107 (t0) cc_final: 0.7703 (m-40) REVERT: A 645 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7750 (mmmt) REVERT: B 328 GLU cc_start: 0.8330 (mp0) cc_final: 0.8084 (mp0) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.0944 time to fit residues: 9.8236 Evaluate side-chains 77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 31 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 40 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.112004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.091732 restraints weight = 7696.228| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.34 r_work: 0.2719 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 7186 Z= 0.091 Angle : 0.491 8.222 9776 Z= 0.243 Chirality : 0.041 0.181 1014 Planarity : 0.004 0.035 1240 Dihedral : 9.517 86.647 962 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.66 % Allowed : 7.71 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.40 (0.29), residues: 834 helix: 1.75 (0.31), residues: 298 sheet: 0.30 (0.53), residues: 98 loop : 0.65 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 667 TYR 0.008 0.001 TYR B 366 PHE 0.023 0.001 PHE A 355 TRP 0.009 0.001 TRP B 676 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7180) covalent geometry : angle 0.48462 ( 9770) hydrogen bonds : bond 0.03448 ( 295) hydrogen bonds : angle 4.24546 ( 738) metal coordination : bond 0.00179 ( 4) metal coordination : angle 3.20708 ( 6) Misc. bond : bond 0.00657 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.179 Fit side-chains REVERT: A 353 GLN cc_start: 0.8566 (mt0) cc_final: 0.8328 (mt0) REVERT: A 645 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7710 (mmmt) REVERT: B 378 MET cc_start: 0.7948 (mmm) cc_final: 0.7654 (mmm) REVERT: B 383 GLU cc_start: 0.8401 (tt0) cc_final: 0.8195 (tt0) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.0794 time to fit residues: 8.0488 Evaluate side-chains 74 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain B residue 466 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.083999 restraints weight = 7945.399| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.51 r_work: 0.2680 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7186 Z= 0.165 Angle : 0.598 16.120 9776 Z= 0.277 Chirality : 0.044 0.154 1014 Planarity : 0.004 0.035 1240 Dihedral : 10.376 92.607 962 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.73 % Allowed : 7.85 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.16 (0.29), residues: 834 helix: 1.55 (0.30), residues: 298 sheet: 0.06 (0.52), residues: 96 loop : 0.53 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 667 TYR 0.009 0.001 TYR B 366 PHE 0.022 0.002 PHE A 355 TRP 0.010 0.001 TRP B 587 HIS 0.007 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 7180) covalent geometry : angle 0.59313 ( 9770) hydrogen bonds : bond 0.04602 ( 295) hydrogen bonds : angle 4.45670 ( 738) metal coordination : bond 0.00301 ( 4) metal coordination : angle 3.20622 ( 6) Misc. bond : bond 0.01188 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.281 Fit side-chains REVERT: A 328 GLU cc_start: 0.7947 (mp0) cc_final: 0.7523 (mp0) REVERT: A 332 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8169 (mtm) REVERT: A 353 GLN cc_start: 0.8583 (mt0) cc_final: 0.8370 (mt0) REVERT: A 608 GLU cc_start: 0.7894 (tt0) cc_final: 0.7424 (mp0) REVERT: A 645 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7776 (mmmt) REVERT: B 383 GLU cc_start: 0.8344 (tt0) cc_final: 0.8100 (tt0) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1164 time to fit residues: 11.9236 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 71.603 > 50: distance: 10 - 15: 23.254 distance: 15 - 16: 25.769 distance: 16 - 17: 43.222 distance: 16 - 19: 32.899 distance: 17 - 18: 49.641 distance: 17 - 26: 34.701 distance: 19 - 20: 49.465 distance: 20 - 21: 39.506 distance: 21 - 22: 40.055 distance: 22 - 23: 31.613 distance: 23 - 24: 39.795 distance: 23 - 25: 38.675 distance: 26 - 27: 35.736 distance: 27 - 28: 55.990 distance: 27 - 30: 40.827 distance: 28 - 29: 24.526 distance: 28 - 36: 55.963 distance: 30 - 31: 55.597 distance: 31 - 32: 40.570 distance: 32 - 34: 39.633 distance: 33 - 35: 13.146 distance: 34 - 35: 30.728 distance: 36 - 37: 56.603 distance: 36 - 42: 51.951 distance: 37 - 38: 29.446 distance: 37 - 40: 45.005 distance: 38 - 39: 31.281 distance: 38 - 43: 42.744 distance: 40 - 41: 41.662 distance: 41 - 42: 49.416 distance: 43 - 44: 40.826 distance: 44 - 45: 51.210 distance: 44 - 47: 63.587 distance: 45 - 46: 50.142 distance: 45 - 52: 24.832 distance: 47 - 48: 48.251 distance: 48 - 49: 30.027 distance: 49 - 50: 27.013 distance: 50 - 51: 49.242 distance: 52 - 53: 36.396 distance: 53 - 54: 42.319 distance: 53 - 56: 24.757 distance: 54 - 55: 39.054 distance: 54 - 63: 32.314 distance: 56 - 57: 33.322 distance: 57 - 58: 35.788 distance: 57 - 59: 16.308 distance: 58 - 60: 25.157 distance: 59 - 61: 29.608 distance: 60 - 62: 36.984 distance: 61 - 62: 44.643 distance: 63 - 64: 21.996 distance: 64 - 65: 34.197 distance: 64 - 67: 44.695 distance: 65 - 66: 34.468 distance: 65 - 71: 49.045 distance: 67 - 68: 39.279 distance: 68 - 69: 41.337 distance: 71 - 72: 43.884 distance: 72 - 73: 15.512 distance: 72 - 75: 61.245 distance: 73 - 74: 18.023 distance: 73 - 85: 38.863 distance: 74 - 105: 16.813 distance: 75 - 76: 38.912 distance: 76 - 77: 40.608 distance: 76 - 78: 21.369 distance: 77 - 79: 27.141 distance: 78 - 80: 14.839 distance: 78 - 81: 26.647 distance: 79 - 80: 28.875 distance: 80 - 82: 46.532 distance: 81 - 83: 39.103 distance: 82 - 84: 3.772 distance: 83 - 84: 42.205 distance: 85 - 86: 56.994 distance: 86 - 87: 54.054 distance: 87 - 88: 30.783 distance: 87 - 96: 34.159 distance: 88 - 113: 32.109 distance: 89 - 90: 55.646 distance: 90 - 91: 35.672 distance: 90 - 92: 35.014 distance: 91 - 93: 27.124 distance: 92 - 94: 49.391 distance: 93 - 95: 14.914 distance: 94 - 95: 20.934 distance: 96 - 97: 16.364 distance: 97 - 98: 39.671 distance: 97 - 100: 40.779 distance: 98 - 99: 56.403 distance: 98 - 105: 39.827 distance: 99 - 121: 34.534 distance: 100 - 101: 43.100 distance: 101 - 102: 18.263 distance: 102 - 103: 32.652 distance: 103 - 104: 16.777 distance: 105 - 106: 41.066 distance: 106 - 107: 36.581 distance: 106 - 109: 58.005 distance: 107 - 108: 40.167 distance: 107 - 113: 22.566 distance: 109 - 110: 40.480 distance: 110 - 111: 45.628 distance: 110 - 112: 55.490