Starting phenix.real_space_refine on Sat Aug 23 10:09:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5d_12026/08_2025/7b5d_12026.cif" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7470 2.51 5 N 1888 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 11462 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5731 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 30, 'TRANS': 670} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 3.54, per 1000 atoms: 0.31 Number of scatterers: 11462 At special positions: 0 Unit cell: (107.272, 116.38, 115.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2032 8.00 N 1888 7.00 C 7470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=2.04 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: 0.82 Conformation dependent library (CDL) restraints added in 397.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 61.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.157A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 242 through 257 Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 325 through 360 removed outlier: 3.923A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.594A pdb=" N MET A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 369 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 406 through 439 removed outlier: 4.233A pdb=" N VAL A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 490 through 519 removed outlier: 4.418A pdb=" N SER A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 567 removed outlier: 4.303A pdb=" N GLU A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 601 Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 630 through 651 removed outlier: 4.704A pdb=" N GLN A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLN A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 699 through 717 removed outlier: 3.876A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 745 removed outlier: 3.507A pdb=" N PHE A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.199A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 854 through 886 removed outlier: 3.887A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 910 Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.157A pdb=" N MET B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 242 through 257 Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 316 through 325 Processing helix chain 'B' and resid 325 through 360 removed outlier: 3.923A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.594A pdb=" N MET B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 406 through 439 removed outlier: 4.234A pdb=" N VAL B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 490 through 519 removed outlier: 4.418A pdb=" N SER B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 567 removed outlier: 4.303A pdb=" N GLU B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 601 Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 630 through 651 removed outlier: 4.704A pdb=" N GLN B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 Processing helix chain 'B' and resid 699 through 717 removed outlier: 3.876A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 745 removed outlier: 3.507A pdb=" N PHE B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.200A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 854 through 886 removed outlier: 3.887A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 910 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.779A pdb=" N THR A 187 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 123 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 279 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.020A pdb=" N TRP A 389 " --> pdb=" O MET A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.975A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.778A pdb=" N THR B 187 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 123 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 279 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA8, first strand: chain 'B' and resid 377 through 378 removed outlier: 4.021A pdb=" N TRP B 389 " --> pdb=" O MET B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.975A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 810 through 813 652 hydrogen bonds defined for protein. 1944 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: 1.58 Time building geometry restraints manager: 1.13 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: 3559 1.34 - 1.46: 2753 1.46 - 1.58: 5322 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11752 Sorted by residual: bond pdb=" C ILE A 786 " pdb=" N PRO A 787 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.49e+00 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.350 -0.015 1.23e-02 6.61e+03 1.44e+00 bond pdb=" C ILE B 343 " pdb=" N PRO B 344 " ideal model delta sigma weight residual 1.336 1.350 -0.015 1.23e-02 6.61e+03 1.44e+00 bond pdb=" CB GLN A 896 " pdb=" CG GLN A 896 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" C ILE B 786 " pdb=" N PRO B 787 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.43e+00 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15754 3.25 - 6.50: 127 6.50 - 9.75: 25 9.75 - 13.00: 0 13.00 - 16.25: 2 Bond angle restraints: 15908 Sorted by residual: angle pdb=" CA LEU A 381 " pdb=" CB LEU A 381 " pdb=" CG LEU A 381 " ideal model delta sigma weight residual 116.30 132.55 -16.25 3.50e+00 8.16e-02 2.15e+01 angle pdb=" CA LEU B 381 " pdb=" CB LEU B 381 " pdb=" CG LEU B 381 " ideal model delta sigma weight residual 116.30 132.50 -16.20 3.50e+00 8.16e-02 2.14e+01 angle pdb=" CA CYS B 625 " pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " ideal model delta sigma weight residual 114.40 122.49 -8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA CYS A 625 " pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " ideal model delta sigma weight residual 114.40 122.44 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" C TYR B 288 " pdb=" N GLU B 289 " pdb=" CA GLU B 289 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 ... (remaining 15903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6166 17.68 - 35.36: 700 35.36 - 53.04: 118 53.04 - 70.72: 32 70.72 - 88.40: 6 Dihedral angle restraints: 7022 sinusoidal: 2870 harmonic: 4152 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 386 " pdb=" CB CYS B 386 " ideal model delta sinusoidal sigma weight residual -86.00 -139.55 53.55 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -139.55 53.55 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual -86.00 -38.37 -47.63 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1252 0.048 - 0.096: 375 0.096 - 0.144: 109 0.144 - 0.191: 14 0.191 - 0.239: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL B 750 " pdb=" CA VAL B 750 " pdb=" CG1 VAL B 750 " pdb=" CG2 VAL B 750 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1749 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 203 " 0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 204 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 203 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 204 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 609 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 610 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.037 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1905 2.76 - 3.30: 10971 3.30 - 3.83: 18889 3.83 - 4.37: 21475 4.37 - 4.90: 37496 Nonbonded interactions: 90736 Sorted by model distance: nonbonded pdb=" O VAL B 590 " pdb=" OG1 THR B 594 " model vdw 2.225 3.040 nonbonded pdb=" O VAL A 590 " pdb=" OG1 THR A 594 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A 406 " pdb=" OG1 THR A 409 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASN B 406 " pdb=" OG1 THR B 409 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR A 331 " pdb=" OD2 ASP A 738 " model vdw 2.331 3.040 ... (remaining 90731 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.120 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.100 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.005 0.059 11760 Z= 0.224 Angle : 0.839 16.246 15924 Z= 0.452 Chirality : 0.049 0.239 1752 Planarity : 0.007 0.084 1998 Dihedral : 15.096 88.397 4310 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.96 % Allowed : 6.98 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.18), residues: 1382 helix: -1.66 (0.14), residues: 832 sheet: -3.02 (0.66), residues: 44 loop : -3.36 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 621 TYR 0.023 0.002 TYR B 119 PHE 0.024 0.002 PHE A 817 TRP 0.021 0.002 TRP A 427 HIS 0.005 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00515 (11752) covalent geometry : angle 0.83702 (15908) SS BOND : bond 0.00392 ( 8) SS BOND : angle 2.18447 ( 16) hydrogen bonds : bond 0.08138 ( 652) hydrogen bonds : angle 5.32113 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.6995 (ttt) cc_final: 0.6536 (ttp) REVERT: A 500 MET cc_start: 0.6870 (mmt) cc_final: 0.5881 (mtp) REVERT: A 505 PHE cc_start: 0.7435 (t80) cc_final: 0.7037 (t80) REVERT: A 704 MET cc_start: 0.7669 (tpp) cc_final: 0.7168 (ttm) REVERT: A 906 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: B 117 MET cc_start: 0.6517 (ttt) cc_final: 0.6087 (ttp) REVERT: B 233 ASP cc_start: 0.5718 (m-30) cc_final: 0.5485 (m-30) REVERT: B 462 VAL cc_start: 0.4170 (OUTLIER) cc_final: 0.3925 (t) REVERT: B 500 MET cc_start: 0.6477 (mmt) cc_final: 0.5752 (mtp) REVERT: B 706 MET cc_start: 0.8315 (mmp) cc_final: 0.8089 (mmp) REVERT: B 753 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7089 (mtp180) REVERT: B 794 MET cc_start: 0.7235 (mtt) cc_final: 0.7008 (mtp) REVERT: B 876 MET cc_start: 0.6786 (mtm) cc_final: 0.6581 (ptt) outliers start: 12 outliers final: 0 residues processed: 206 average time/residue: 0.1168 time to fit residues: 32.3626 Evaluate side-chains 154 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain B residue 462 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 406 ASN A 709 GLN A 730 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124917 restraints weight = 13090.868| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.53 r_work: 0.3155 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11760 Z= 0.172 Angle : 0.632 11.677 15924 Z= 0.323 Chirality : 0.042 0.134 1752 Planarity : 0.005 0.078 1998 Dihedral : 5.245 67.613 1550 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.36 % Allowed : 12.92 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.21), residues: 1382 helix: 0.03 (0.17), residues: 834 sheet: -3.17 (0.63), residues: 44 loop : -2.99 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 125 TYR 0.018 0.001 TYR B 119 PHE 0.018 0.002 PHE B 505 TRP 0.017 0.001 TRP B 427 HIS 0.004 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00412 (11752) covalent geometry : angle 0.63102 (15908) SS BOND : bond 0.00379 ( 8) SS BOND : angle 1.45748 ( 16) hydrogen bonds : bond 0.04209 ( 652) hydrogen bonds : angle 4.42895 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7399 (ttt) cc_final: 0.6581 (ttp) REVERT: A 219 ARG cc_start: 0.4810 (mmt180) cc_final: 0.4600 (mmm160) REVERT: A 505 PHE cc_start: 0.7697 (t80) cc_final: 0.7230 (t80) REVERT: A 704 MET cc_start: 0.8577 (tpp) cc_final: 0.8130 (ttm) REVERT: A 734 GLU cc_start: 0.8461 (tp30) cc_final: 0.8186 (tp30) REVERT: A 784 ASP cc_start: 0.8664 (t0) cc_final: 0.8386 (t0) REVERT: B 117 MET cc_start: 0.6816 (ttt) cc_final: 0.6197 (ttp) REVERT: B 416 MET cc_start: 0.8967 (tpt) cc_final: 0.8597 (mmp) REVERT: B 500 MET cc_start: 0.6405 (mmt) cc_final: 0.5243 (mtp) REVERT: B 505 PHE cc_start: 0.7362 (t80) cc_final: 0.6978 (t80) REVERT: B 753 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7439 (mtp180) REVERT: B 801 MET cc_start: 0.8365 (mtm) cc_final: 0.8124 (mtm) outliers start: 17 outliers final: 5 residues processed: 180 average time/residue: 0.1453 time to fit residues: 35.1186 Evaluate side-chains 161 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 406 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130526 restraints weight = 13197.482| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.49 r_work: 0.3178 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11760 Z= 0.130 Angle : 0.588 11.566 15924 Z= 0.298 Chirality : 0.040 0.146 1752 Planarity : 0.005 0.076 1998 Dihedral : 4.580 21.543 1546 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.52 % Allowed : 14.93 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.22), residues: 1382 helix: 0.72 (0.17), residues: 836 sheet: -3.26 (0.56), residues: 44 loop : -2.78 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 128 TYR 0.016 0.001 TYR B 119 PHE 0.016 0.001 PHE B 589 TRP 0.015 0.001 TRP B 427 HIS 0.003 0.001 HIS A 898 Details of bonding type rmsd covalent geometry : bond 0.00297 (11752) covalent geometry : angle 0.58407 (15908) SS BOND : bond 0.00659 ( 8) SS BOND : angle 2.12538 ( 16) hydrogen bonds : bond 0.03837 ( 652) hydrogen bonds : angle 4.25680 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7317 (ttt) cc_final: 0.6543 (ttp) REVERT: A 219 ARG cc_start: 0.4908 (mmt180) cc_final: 0.4362 (mmm160) REVERT: A 233 ASP cc_start: 0.6136 (m-30) cc_final: 0.5778 (t70) REVERT: A 416 MET cc_start: 0.8946 (tpt) cc_final: 0.8557 (tpt) REVERT: A 505 PHE cc_start: 0.7607 (t80) cc_final: 0.7169 (t80) REVERT: A 704 MET cc_start: 0.8620 (tpp) cc_final: 0.8191 (ttm) REVERT: A 734 GLU cc_start: 0.8402 (tp30) cc_final: 0.8167 (tp30) REVERT: A 769 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7439 (tttt) REVERT: A 784 ASP cc_start: 0.8773 (t0) cc_final: 0.8364 (t0) REVERT: B 215 GLN cc_start: 0.7566 (pt0) cc_final: 0.7183 (mt0) REVERT: B 233 ASP cc_start: 0.5996 (m-30) cc_final: 0.5201 (t70) REVERT: B 416 MET cc_start: 0.8915 (tpt) cc_final: 0.8577 (tpt) REVERT: B 500 MET cc_start: 0.6515 (mmt) cc_final: 0.5324 (mtp) REVERT: B 505 PHE cc_start: 0.7302 (t80) cc_final: 0.6964 (t80) REVERT: B 753 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7420 (mtp180) outliers start: 19 outliers final: 9 residues processed: 183 average time/residue: 0.1453 time to fit residues: 35.6629 Evaluate side-chains 173 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134604 restraints weight = 13147.443| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.49 r_work: 0.3196 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11760 Z= 0.125 Angle : 0.568 11.182 15924 Z= 0.286 Chirality : 0.040 0.151 1752 Planarity : 0.004 0.075 1998 Dihedral : 4.409 17.191 1546 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.36 % Allowed : 17.09 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.22), residues: 1382 helix: 1.05 (0.18), residues: 828 sheet: -3.29 (0.55), residues: 44 loop : -2.64 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 127 TYR 0.015 0.001 TYR B 119 PHE 0.016 0.001 PHE B 589 TRP 0.014 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00283 (11752) covalent geometry : angle 0.56542 (15908) SS BOND : bond 0.00233 ( 8) SS BOND : angle 1.65885 ( 16) hydrogen bonds : bond 0.03695 ( 652) hydrogen bonds : angle 4.16575 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5091 (mmt180) cc_final: 0.4560 (mmm160) REVERT: A 233 ASP cc_start: 0.6064 (m-30) cc_final: 0.5797 (t70) REVERT: A 416 MET cc_start: 0.8928 (tpt) cc_final: 0.8465 (tpt) REVERT: A 505 PHE cc_start: 0.7583 (t80) cc_final: 0.7153 (t80) REVERT: A 704 MET cc_start: 0.8614 (tpp) cc_final: 0.8205 (ttm) REVERT: A 734 GLU cc_start: 0.8281 (tp30) cc_final: 0.8060 (tp30) REVERT: B 215 GLN cc_start: 0.7421 (pt0) cc_final: 0.7026 (mt0) REVERT: B 233 ASP cc_start: 0.6109 (m-30) cc_final: 0.5250 (t70) REVERT: B 416 MET cc_start: 0.8913 (tpt) cc_final: 0.8508 (tpt) REVERT: B 505 PHE cc_start: 0.7298 (t80) cc_final: 0.6877 (t80) REVERT: B 753 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7405 (mtp180) REVERT: B 769 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.6642 (ttpt) outliers start: 17 outliers final: 10 residues processed: 185 average time/residue: 0.1313 time to fit residues: 32.7787 Evaluate side-chains 173 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 406 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135572 restraints weight = 12953.332| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.36 r_work: 0.3199 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11760 Z= 0.154 Angle : 0.583 11.343 15924 Z= 0.296 Chirality : 0.041 0.156 1752 Planarity : 0.004 0.074 1998 Dihedral : 4.397 19.183 1546 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.52 % Allowed : 18.38 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.22), residues: 1382 helix: 1.14 (0.18), residues: 826 sheet: -3.47 (0.52), residues: 44 loop : -2.57 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.015 0.001 TYR B 119 PHE 0.015 0.001 PHE B 589 TRP 0.013 0.001 TRP B 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00366 (11752) covalent geometry : angle 0.58132 (15908) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.35136 ( 16) hydrogen bonds : bond 0.03838 ( 652) hydrogen bonds : angle 4.18329 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.4998 (mmt180) cc_final: 0.4483 (mmm160) REVERT: A 416 MET cc_start: 0.8959 (tpt) cc_final: 0.8478 (tpt) REVERT: A 505 PHE cc_start: 0.7571 (t80) cc_final: 0.7094 (t80) REVERT: A 734 GLU cc_start: 0.8283 (tp30) cc_final: 0.8074 (tp30) REVERT: B 215 GLN cc_start: 0.7449 (pt0) cc_final: 0.7073 (mt0) REVERT: B 233 ASP cc_start: 0.5959 (m-30) cc_final: 0.5267 (t70) REVERT: B 416 MET cc_start: 0.8971 (tpt) cc_final: 0.8512 (tpt) REVERT: B 500 MET cc_start: 0.6543 (mmt) cc_final: 0.5286 (mtp) REVERT: B 505 PHE cc_start: 0.7234 (t80) cc_final: 0.6790 (t80) REVERT: B 753 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7401 (mtp180) REVERT: B 769 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.6640 (ttpt) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 0.1308 time to fit residues: 31.9598 Evaluate side-chains 172 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 131 optimal weight: 0.0020 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN A 709 GLN A 730 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 730 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127937 restraints weight = 13366.367| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.40 r_work: 0.3144 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11760 Z= 0.183 Angle : 0.619 11.538 15924 Z= 0.315 Chirality : 0.042 0.168 1752 Planarity : 0.005 0.075 1998 Dihedral : 4.503 23.964 1546 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.93 % Allowed : 19.02 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1382 helix: 1.17 (0.18), residues: 822 sheet: -3.67 (0.49), residues: 44 loop : -2.42 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 127 TYR 0.015 0.001 TYR B 119 PHE 0.016 0.001 PHE A 785 TRP 0.013 0.001 TRP B 427 HIS 0.005 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00440 (11752) covalent geometry : angle 0.61503 (15908) SS BOND : bond 0.00213 ( 8) SS BOND : angle 2.17895 ( 16) hydrogen bonds : bond 0.04037 ( 652) hydrogen bonds : angle 4.20685 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.4885 (mmt180) cc_final: 0.4422 (mmm160) REVERT: A 416 MET cc_start: 0.9006 (tpt) cc_final: 0.8514 (tpt) REVERT: A 505 PHE cc_start: 0.7564 (t80) cc_final: 0.7106 (t80) REVERT: B 213 ARG cc_start: 0.7500 (ptt-90) cc_final: 0.7295 (ptt-90) REVERT: B 215 GLN cc_start: 0.7589 (pt0) cc_final: 0.7203 (mt0) REVERT: B 219 ARG cc_start: 0.4663 (mmm160) cc_final: 0.4416 (mmm160) REVERT: B 233 ASP cc_start: 0.5978 (m-30) cc_final: 0.5284 (t70) REVERT: B 416 MET cc_start: 0.9026 (tpt) cc_final: 0.8544 (tpt) REVERT: B 505 PHE cc_start: 0.7374 (t80) cc_final: 0.6962 (t80) REVERT: B 753 ARG cc_start: 0.7933 (mtp180) cc_final: 0.7436 (mtp180) REVERT: B 769 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.6674 (ttpt) outliers start: 24 outliers final: 16 residues processed: 183 average time/residue: 0.1346 time to fit residues: 32.9187 Evaluate side-chains 177 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 709 GLN A 730 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN B 730 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.134215 restraints weight = 13095.533| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.66 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11760 Z= 0.126 Angle : 0.577 11.057 15924 Z= 0.292 Chirality : 0.040 0.163 1752 Planarity : 0.004 0.076 1998 Dihedral : 4.383 24.411 1546 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.69 % Allowed : 19.10 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1382 helix: 1.37 (0.18), residues: 822 sheet: -3.63 (0.52), residues: 44 loop : -2.39 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 TYR 0.014 0.001 TYR A 119 PHE 0.015 0.001 PHE A 589 TRP 0.015 0.001 TRP B 427 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00287 (11752) covalent geometry : angle 0.57285 (15908) SS BOND : bond 0.00361 ( 8) SS BOND : angle 2.23120 ( 16) hydrogen bonds : bond 0.03691 ( 652) hydrogen bonds : angle 4.12343 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.5067 (mmt180) cc_final: 0.4409 (mmm160) REVERT: A 233 ASP cc_start: 0.4936 (t70) cc_final: 0.4666 (t0) REVERT: A 416 MET cc_start: 0.8915 (tpt) cc_final: 0.8402 (tpt) REVERT: A 505 PHE cc_start: 0.7555 (t80) cc_final: 0.7110 (t80) REVERT: B 215 GLN cc_start: 0.7454 (pt0) cc_final: 0.7069 (mt0) REVERT: B 219 ARG cc_start: 0.4779 (mmm160) cc_final: 0.4495 (mmm160) REVERT: B 228 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7644 (ttpt) REVERT: B 233 ASP cc_start: 0.5529 (m-30) cc_final: 0.5276 (t70) REVERT: B 416 MET cc_start: 0.8949 (tpt) cc_final: 0.8452 (tpt) REVERT: B 500 MET cc_start: 0.6552 (mmt) cc_final: 0.5267 (mtp) REVERT: B 505 PHE cc_start: 0.7287 (t80) cc_final: 0.6908 (t80) REVERT: B 649 GLN cc_start: 0.2034 (OUTLIER) cc_final: 0.1388 (pt0) REVERT: B 753 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7466 (mtp180) REVERT: B 769 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6620 (ttpt) outliers start: 21 outliers final: 17 residues processed: 186 average time/residue: 0.1294 time to fit residues: 32.3328 Evaluate side-chains 183 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 795 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 67.2475 > 50: distance: 89 - 123: 14.357 distance: 99 - 103: 25.935 distance: 104 - 105: 17.040 distance: 105 - 106: 35.539 distance: 105 - 114: 15.072 distance: 107 - 108: 16.198 distance: 108 - 109: 9.418 distance: 109 - 110: 16.522 distance: 110 - 111: 8.396 distance: 111 - 112: 10.360 distance: 111 - 113: 28.180 distance: 114 - 115: 13.881 distance: 115 - 116: 25.793 distance: 115 - 118: 10.108 distance: 116 - 117: 17.250 distance: 116 - 120: 16.105 distance: 118 - 119: 13.670 distance: 120 - 121: 10.168 distance: 121 - 122: 14.127 distance: 121 - 124: 21.768 distance: 122 - 123: 16.433 distance: 122 - 131: 10.204 distance: 124 - 125: 7.523 distance: 125 - 126: 16.925 distance: 125 - 127: 5.007 distance: 126 - 128: 4.832 distance: 127 - 129: 8.824 distance: 128 - 130: 14.775 distance: 129 - 130: 17.803 distance: 131 - 132: 7.195 distance: 132 - 133: 13.039 distance: 132 - 135: 14.153 distance: 133 - 134: 16.582 distance: 133 - 142: 8.905 distance: 135 - 136: 26.364 distance: 136 - 137: 27.217 distance: 137 - 138: 17.441 distance: 138 - 139: 11.932 distance: 139 - 140: 21.275 distance: 139 - 141: 24.446 distance: 142 - 143: 25.715 distance: 143 - 144: 16.823 distance: 143 - 146: 11.256 distance: 144 - 145: 39.827 distance: 144 - 150: 15.530 distance: 146 - 147: 9.614 distance: 147 - 148: 10.726 distance: 148 - 149: 7.659 distance: 150 - 151: 5.260 distance: 151 - 152: 21.015 distance: 151 - 154: 7.008 distance: 152 - 153: 12.202 distance: 152 - 159: 20.295 distance: 154 - 155: 28.193 distance: 155 - 156: 19.840 distance: 156 - 157: 25.176 distance: 156 - 158: 24.991 distance: 159 - 160: 22.608 distance: 160 - 161: 7.233 distance: 160 - 163: 11.883 distance: 161 - 162: 12.966 distance: 161 - 168: 22.206 distance: 163 - 164: 10.259 distance: 164 - 165: 44.923 distance: 165 - 166: 24.602 distance: 165 - 167: 24.481 distance: 168 - 169: 5.647 distance: 169 - 170: 8.195 distance: 169 - 172: 11.618 distance: 170 - 171: 7.192 distance: 170 - 174: 12.485 distance: 172 - 173: 8.384 distance: 173 - 197: 26.629 distance: 174 - 175: 24.296 distance: 175 - 176: 11.773 distance: 175 - 178: 13.627 distance: 176 - 177: 12.323 distance: 176 - 179: 18.056 distance: 179 - 180: 39.678 distance: 179 - 185: 11.050 distance: 180 - 181: 39.474 distance: 180 - 183: 3.271 distance: 181 - 182: 5.287 distance: 181 - 186: 31.579 distance: 183 - 184: 16.159 distance: 184 - 185: 28.400