Starting phenix.real_space_refine on Mon Nov 17 16:35:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzz_34406/11_2025/8gzz_34406.map" } resolution = 3.52 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= -0.003 sd= 0.027 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 36 5.16 5 C 4186 2.51 5 N 1084 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 1.96, per 1000 atoms: 0.30 Number of scatterers: 6568 At special positions: 0 Unit cell: (87.36, 130.624, 79.04, 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 36 16.00 O 1262 8.00 N 1084 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 469.9 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 17 sheets defined 9.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.523A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.914A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.056A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.508A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.868A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.092A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.981A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.572A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.575A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.741A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.609A pdb=" N GLU D 13 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.717A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.668A pdb=" N GLU F 13 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.738A pdb=" N THR G 20 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 60 through 61 removed outlier: 6.646A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 459 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: 1.02 Time building geometry restraints manager: 0.74 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: 2082 1.34 - 1.47: 1820 1.47 - 1.59: 2798 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 6742 Sorted by residual: bond pdb=" C LYS A 356 " pdb=" N ARG A 357 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.32e-02 5.74e+03 1.02e+01 bond pdb=" C GLN F 24 " pdb=" N ALA F 25 " ideal model delta sigma weight residual 1.329 1.285 0.044 1.44e-02 4.82e+03 9.46e+00 bond pdb=" C CYS F 23 " pdb=" N GLN F 24 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" N GLN F 24 " pdb=" CA GLN F 24 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.79e+00 ... (remaining 6737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 8628 1.15 - 2.31: 435 2.31 - 3.46: 91 3.46 - 4.62: 24 4.62 - 5.77: 6 Bond angle restraints: 9184 Sorted by residual: angle pdb=" C TYR F 49 " pdb=" CA TYR F 49 " pdb=" CB TYR F 49 " ideal model delta sigma weight residual 109.80 115.57 -5.77 1.65e+00 3.67e-01 1.22e+01 angle pdb=" C LYS A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 123.00 118.33 4.67 1.38e+00 5.25e-01 1.15e+01 angle pdb=" CA GLN A 414 " pdb=" C GLN A 414 " pdb=" O GLN A 414 " ideal model delta sigma weight residual 121.56 118.05 3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" N TYR F 49 " pdb=" CA TYR F 49 " pdb=" C TYR F 49 " ideal model delta sigma weight residual 110.42 105.78 4.64 1.55e+00 4.16e-01 8.96e+00 angle pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" C PHE A 377 " ideal model delta sigma weight residual 112.72 109.48 3.24 1.14e+00 7.69e-01 8.09e+00 ... (remaining 9179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3617 17.80 - 35.61: 289 35.61 - 53.41: 29 53.41 - 71.22: 7 71.22 - 89.02: 4 Dihedral angle restraints: 3946 sinusoidal: 1490 harmonic: 2456 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 24.54 68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 26.66 66.34 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 529 0.030 - 0.059: 314 0.059 - 0.089: 88 0.089 - 0.118: 57 0.118 - 0.148: 12 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLN F 24 " pdb=" N GLN F 24 " pdb=" C GLN F 24 " pdb=" CB GLN F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA GLU B 465 " pdb=" N GLU B 465 " pdb=" C GLU B 465 " pdb=" CB GLU B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 997 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 48 " -0.007 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C ILE F 48 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE F 48 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR F 49 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 24 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.21e+00 pdb=" C GLN F 24 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN F 24 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA F 25 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 49 " -0.012 2.00e-02 2.50e+03 9.52e-03 1.81e+00 pdb=" CG TYR D 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 49 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1441 2.78 - 3.31: 5887 3.31 - 3.84: 10276 3.84 - 4.37: 12188 4.37 - 4.90: 21752 Nonbonded interactions: 51544 Sorted by model distance: nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR G 103 " model vdw 2.248 3.040 nonbonded pdb=" O SER E 29 " pdb=" OG1 THR E 53 " model vdw 2.299 3.040 nonbonded pdb=" O SER G 29 " pdb=" OG1 THR G 53 " model vdw 2.334 3.040 nonbonded pdb=" NE2 GLN F 90 " pdb=" O SER F 93 " model vdw 2.337 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.340 3.040 ... (remaining 51539 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' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.280 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.090 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.004 0.044 6756 Z= 0.227 Angle : 0.621 5.770 9212 Z= 0.362 Chirality : 0.044 0.148 1000 Planarity : 0.003 0.028 1184 Dihedral : 12.188 89.023 2348 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 are not related in a simple way. whole: -0.99 (0.28), residues: 842 helix: -3.59 (0.49), residues: 54 sheet: 0.41 (0.33), residues: 264 loop : -0.90 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.023 0.001 TYR D 49 PHE 0.021 0.002 PHE A 347 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 6742) covalent geometry : angle 0.61966 ( 9184) SS BOND : bond 0.00294 ( 14) SS BOND : angle 1.03895 ( 28) hydrogen bonds : bond 0.18472 ( 186) hydrogen bonds : angle 8.99483 ( 459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.269 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0935 time to fit residues: 13.8647 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 360 ASN D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071194 restraints weight = 16635.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073913 restraints weight = 8081.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075675 restraints weight = 5197.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076812 restraints weight = 3887.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077574 restraints weight = 3188.762| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6756 Z= 0.110 Angle : 0.531 4.968 9212 Z= 0.284 Chirality : 0.042 0.143 1000 Planarity : 0.004 0.038 1184 Dihedral : 4.104 15.967 932 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.99 % Allowed : 7.61 % Favored : 91.41 % 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 are not related in a simple way. whole: -1.02 (0.29), residues: 842 helix: -3.97 (0.42), residues: 54 sheet: 0.26 (0.32), residues: 292 loop : -0.86 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.013 0.001 TYR A 380 PHE 0.043 0.001 PHE B 374 TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6742) covalent geometry : angle 0.52761 ( 9184) SS BOND : bond 0.00468 ( 14) SS BOND : angle 1.17363 ( 28) hydrogen bonds : bond 0.03415 ( 186) hydrogen bonds : angle 6.64664 ( 459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 474 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: B 420 ASP cc_start: 0.8552 (m-30) cc_final: 0.8310 (t0) REVERT: D 82 ASP cc_start: 0.7528 (m-30) cc_final: 0.7117 (m-30) REVERT: D 96 ASP cc_start: 0.8053 (p0) cc_final: 0.7119 (p0) outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 0.0826 time to fit residues: 11.2712 Evaluate side-chains 95 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068295 restraints weight = 16648.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.070899 restraints weight = 7997.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.072578 restraints weight = 5119.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073649 restraints weight = 3824.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074368 restraints weight = 3135.168| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6756 Z= 0.221 Angle : 0.552 4.781 9212 Z= 0.297 Chirality : 0.044 0.140 1000 Planarity : 0.004 0.034 1184 Dihedral : 4.313 16.515 932 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.11 % Allowed : 9.86 % Favored : 88.03 % 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 are not related in a simple way. whole: -1.14 (0.29), residues: 842 helix: -3.97 (0.44), residues: 54 sheet: 0.10 (0.31), residues: 296 loop : -0.89 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.011 0.001 TYR A 380 PHE 0.013 0.001 PHE E 95 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 6742) covalent geometry : angle 0.54809 ( 9184) SS BOND : bond 0.00417 ( 14) SS BOND : angle 1.24752 ( 28) hydrogen bonds : bond 0.03406 ( 186) hydrogen bonds : angle 6.49826 ( 459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8792 (m) cc_final: 0.8162 (p) REVERT: B 420 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (t0) REVERT: D 96 ASP cc_start: 0.8097 (p0) cc_final: 0.7174 (p0) outliers start: 15 outliers final: 9 residues processed: 101 average time/residue: 0.0780 time to fit residues: 10.9666 Evaluate side-chains 102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 505 HIS B 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.069161 restraints weight = 16819.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071810 restraints weight = 8018.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073521 restraints weight = 5094.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074631 restraints weight = 3788.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075374 restraints weight = 3095.142| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6756 Z= 0.151 Angle : 0.512 6.396 9212 Z= 0.276 Chirality : 0.042 0.143 1000 Planarity : 0.004 0.036 1184 Dihedral : 4.191 16.503 932 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.83 % Allowed : 13.38 % Favored : 84.79 % 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 are not related in a simple way. whole: -1.28 (0.28), residues: 842 helix: -4.06 (0.41), residues: 54 sheet: -0.07 (0.32), residues: 278 loop : -0.91 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.010 0.001 TYR A 380 PHE 0.010 0.001 PHE A 347 TRP 0.013 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6742) covalent geometry : angle 0.50941 ( 9184) SS BOND : bond 0.00411 ( 14) SS BOND : angle 1.11232 ( 28) hydrogen bonds : bond 0.02898 ( 186) hydrogen bonds : angle 6.19794 ( 459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8284 (t0) REVERT: D 82 ASP cc_start: 0.7473 (m-30) cc_final: 0.7249 (m-30) REVERT: D 96 ASP cc_start: 0.8094 (p0) cc_final: 0.7180 (p0) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.0831 time to fit residues: 11.2344 Evaluate side-chains 101 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 0.0170 overall best weight: 0.2248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069693 restraints weight = 16884.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072316 restraints weight = 7970.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074028 restraints weight = 5024.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075141 restraints weight = 3711.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075889 restraints weight = 3016.766| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6756 Z= 0.091 Angle : 0.484 5.264 9212 Z= 0.257 Chirality : 0.041 0.134 1000 Planarity : 0.003 0.040 1184 Dihedral : 3.860 15.790 932 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.27 % Allowed : 14.51 % Favored : 84.23 % 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 are not related in a simple way. whole: -0.96 (0.29), residues: 842 helix: -4.13 (0.40), residues: 54 sheet: 0.31 (0.32), residues: 280 loop : -0.77 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 61 TYR 0.012 0.001 TYR A 380 PHE 0.008 0.001 PHE D 62 TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6742) covalent geometry : angle 0.48164 ( 9184) SS BOND : bond 0.00462 ( 14) SS BOND : angle 0.99638 ( 28) hydrogen bonds : bond 0.02500 ( 186) hydrogen bonds : angle 5.84261 ( 459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 THR cc_start: 0.8580 (m) cc_final: 0.8044 (p) REVERT: B 420 ASP cc_start: 0.8578 (m-30) cc_final: 0.8283 (t0) REVERT: D 96 ASP cc_start: 0.8089 (p0) cc_final: 0.7192 (p0) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.0775 time to fit residues: 11.3878 Evaluate side-chains 102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN F 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.081769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067784 restraints weight = 16861.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070385 restraints weight = 7950.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072091 restraints weight = 5034.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.073180 restraints weight = 3730.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.073913 restraints weight = 3035.661| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6756 Z= 0.154 Angle : 0.534 10.662 9212 Z= 0.283 Chirality : 0.042 0.131 1000 Planarity : 0.004 0.042 1184 Dihedral : 4.040 15.599 932 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.11 % Allowed : 15.21 % Favored : 82.68 % 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 are not related in a simple way. whole: -1.26 (0.29), residues: 842 helix: -4.10 (0.41), residues: 54 sheet: -0.15 (0.32), residues: 278 loop : -0.83 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.017 0.001 TYR F 36 PHE 0.011 0.001 PHE E 95 TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6742) covalent geometry : angle 0.53096 ( 9184) SS BOND : bond 0.00415 ( 14) SS BOND : angle 1.10032 ( 28) hydrogen bonds : bond 0.02750 ( 186) hydrogen bonds : angle 5.89788 ( 459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 THR cc_start: 0.8659 (m) cc_final: 0.7974 (p) REVERT: B 420 ASP cc_start: 0.8574 (m-30) cc_final: 0.8280 (t0) REVERT: D 82 ASP cc_start: 0.7367 (m-30) cc_final: 0.7146 (m-30) REVERT: D 96 ASP cc_start: 0.8136 (p0) cc_final: 0.7244 (p0) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.0780 time to fit residues: 11.9501 Evaluate side-chains 103 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 0.0060 chunk 77 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068505 restraints weight = 16658.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.071113 restraints weight = 7850.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072786 restraints weight = 4970.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073888 restraints weight = 3695.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074609 restraints weight = 3014.314| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.112 Angle : 0.518 8.819 9212 Z= 0.272 Chirality : 0.042 0.132 1000 Planarity : 0.004 0.045 1184 Dihedral : 3.981 15.987 932 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.83 % Allowed : 15.35 % Favored : 82.82 % 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 are not related in a simple way. whole: -1.29 (0.28), residues: 842 helix: -4.03 (0.42), residues: 54 sheet: -0.14 (0.32), residues: 268 loop : -0.87 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 95 TYR 0.010 0.001 TYR A 380 PHE 0.008 0.001 PHE E 95 TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6742) covalent geometry : angle 0.51462 ( 9184) SS BOND : bond 0.00447 ( 14) SS BOND : angle 1.16465 ( 28) hydrogen bonds : bond 0.02533 ( 186) hydrogen bonds : angle 5.84781 ( 459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8267 (pt0) cc_final: 0.8024 (pt0) REVERT: B 376 THR cc_start: 0.8604 (m) cc_final: 0.8023 (p) REVERT: B 420 ASP cc_start: 0.8545 (m-30) cc_final: 0.8243 (t0) REVERT: B 474 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8051 (tm-30) REVERT: D 96 ASP cc_start: 0.8089 (p0) cc_final: 0.7192 (p0) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 0.0816 time to fit residues: 11.6289 Evaluate side-chains 105 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068128 restraints weight = 16946.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070754 restraints weight = 8092.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072442 restraints weight = 5175.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073535 restraints weight = 3869.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074252 restraints weight = 3169.572| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6756 Z= 0.129 Angle : 0.521 7.757 9212 Z= 0.275 Chirality : 0.042 0.131 1000 Planarity : 0.004 0.044 1184 Dihedral : 4.003 16.741 932 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 14.65 % Favored : 83.24 % 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 are not related in a simple way. whole: -1.30 (0.28), residues: 842 helix: -4.04 (0.42), residues: 54 sheet: -0.16 (0.32), residues: 278 loop : -0.88 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 454 TYR 0.009 0.001 TYR A 380 PHE 0.009 0.001 PHE E 95 TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6742) covalent geometry : angle 0.51850 ( 9184) SS BOND : bond 0.00426 ( 14) SS BOND : angle 1.00946 ( 28) hydrogen bonds : bond 0.02557 ( 186) hydrogen bonds : angle 5.86706 ( 459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8599 (tptp) cc_final: 0.8209 (ttmm) REVERT: B 340 GLU cc_start: 0.8291 (pt0) cc_final: 0.8050 (pt0) REVERT: B 376 THR cc_start: 0.8650 (m) cc_final: 0.8115 (p) REVERT: B 420 ASP cc_start: 0.8559 (m-30) cc_final: 0.8256 (t0) REVERT: D 96 ASP cc_start: 0.8124 (p0) cc_final: 0.7231 (p0) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.0835 time to fit residues: 12.0481 Evaluate side-chains 108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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-2.0-5881/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: 70.4132 > 50: distance: 17 - 157: 35.185 distance: 18 - 151: 35.709 distance: 21 - 148: 31.822 distance: 73 - 78: 30.699 distance: 78 - 79: 39.398 distance: 79 - 80: 15.676 distance: 79 - 82: 42.451 distance: 80 - 90: 28.807 distance: 82 - 83: 60.823 distance: 83 - 84: 19.603 distance: 83 - 85: 58.052 distance: 85 - 87: 14.609 distance: 87 - 88: 59.638 distance: 90 - 91: 15.027 distance: 91 - 92: 15.729 distance: 91 - 94: 25.526 distance: 92 - 93: 44.538 distance: 92 - 99: 22.391 distance: 94 - 95: 34.325 distance: 95 - 96: 56.859 distance: 96 - 97: 34.768 distance: 97 - 98: 5.278 distance: 99 - 100: 50.610 distance: 100 - 101: 5.712 distance: 101 - 102: 7.867 distance: 101 - 107: 41.262 distance: 103 - 104: 9.340 distance: 104 - 106: 40.741 distance: 107 - 113: 38.986 distance: 109 - 110: 10.645 distance: 109 - 114: 39.155 distance: 111 - 112: 10.650 distance: 112 - 113: 30.236 distance: 115 - 118: 40.773 distance: 118 - 119: 39.613 distance: 119 - 121: 20.716 distance: 123 - 124: 39.264 distance: 123 - 126: 40.190 distance: 124 - 130: 40.789 distance: 126 - 127: 40.767 distance: 127 - 128: 26.474 distance: 131 - 132: 10.198 distance: 131 - 134: 29.955 distance: 132 - 133: 50.348 distance: 132 - 141: 8.795 distance: 134 - 135: 41.950 distance: 135 - 136: 40.376 distance: 135 - 137: 30.652 distance: 138 - 140: 29.607 distance: 139 - 140: 42.137 distance: 141 - 142: 48.017 distance: 142 - 143: 15.125 distance: 142 - 145: 35.670 distance: 143 - 144: 22.236 distance: 143 - 148: 24.221 distance: 145 - 146: 40.257 distance: 145 - 147: 37.733 distance: 148 - 149: 40.298 distance: 149 - 150: 50.932 distance: 150 - 151: 52.019 distance: 150 - 152: 41.872 distance: 152 - 153: 26.526 distance: 152 - 203: 20.181 distance: 153 - 154: 35.958 distance: 153 - 156: 40.045 distance: 154 - 155: 41.065 distance: 154 - 158: 16.045 distance: 155 - 200: 37.779 distance: 156 - 157: 39.202