Starting phenix.real_space_refine on Fri Aug 22 18:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2025/9jhm_61487.cif" } resolution = 3.2 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 35 5.49 5 S 20 5.16 5 C 4244 2.51 5 N 1115 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.26 Number of scatterers: 6755 At special positions: 0 Unit cell: (71.34, 83.64, 102.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 20 16.00 P 35 15.00 O 1340 8.00 N 1115 7.00 C 4244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 351.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 31.4% alpha, 17.6% beta 7 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.926A pdb=" N ASN A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.781A pdb=" N TYR A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.686A pdb=" N TYR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.574A pdb=" N SER A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.642A pdb=" N PHE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 583 through 603 removed outlier: 4.296A pdb=" N LEU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.646A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.519A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.898A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.834A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 83 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.534A pdb=" N TYR A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.563A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 223 removed outlier: 7.230A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.625A pdb=" N SER A 663 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 690 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 641 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A 692 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU A 639 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 694 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 609 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 540 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 569 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 745 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 359 removed outlier: 4.052A pdb=" N GLY A 357 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.483A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 461 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 652 224 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1663 1.33 - 1.45: 1451 1.45 - 1.57: 3745 1.57 - 1.69: 69 1.69 - 1.81: 35 Bond restraints: 6963 Sorted by residual: bond pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.23e-02 6.61e+03 5.63e+00 bond pdb=" CB ASN A 681 " pdb=" CG ASN A 681 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.18e+00 bond pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.49e+00 bond pdb=" CG ARG A 158 " pdb=" CD ARG A 158 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.83e+00 bond pdb=" C3' DT E 12 " pdb=" O3' DT E 12 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.16e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 9135 2.29 - 4.59: 342 4.59 - 6.88: 41 6.88 - 9.17: 16 9.17 - 11.46: 2 Bond angle restraints: 9536 Sorted by residual: angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.82 129.75 -8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C GLY A 264 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C GLU A 680 " pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 123.05 131.19 -8.14 1.57e+00 4.06e-01 2.69e+01 angle pdb=" C LYS A 631 " pdb=" N ASN A 632 " pdb=" CA ASN A 632 " ideal model delta sigma weight residual 122.46 129.45 -6.99 1.41e+00 5.03e-01 2.46e+01 angle pdb=" CA ASN A 681 " pdb=" CB ASN A 681 " pdb=" CG ASN A 681 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 ... (remaining 9531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 3846 24.08 - 48.15: 220 48.15 - 72.23: 59 72.23 - 96.31: 6 96.31 - 120.38: 1 Dihedral angle restraints: 4132 sinusoidal: 1945 harmonic: 2187 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual 180.00 -149.07 -30.93 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA THR A 507 " pdb=" C THR A 507 " pdb=" N ALA A 508 " pdb=" CA ALA A 508 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 764 0.056 - 0.112: 203 0.112 - 0.168: 61 0.168 - 0.225: 9 0.225 - 0.281: 7 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE A 712 " pdb=" CA ILE A 712 " pdb=" CG1 ILE A 712 " pdb=" CG2 ILE A 712 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 520 " pdb=" CB LEU A 520 " pdb=" CD1 LEU A 520 " pdb=" CD2 LEU A 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1041 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C GLU A 470 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 468 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASP A 468 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 468 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 469 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " -0.017 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 623 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.006 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.05: 3767 3.05 - 3.66: 10732 3.66 - 4.28: 15928 4.28 - 4.90: 25357 Nonbonded interactions: 55808 Sorted by model distance: nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.811 2.320 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.863 2.320 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.906 2.320 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 2.066 2.320 nonbonded pdb=" O ILE A 515 " pdb=" CG1 ILE A 519 " model vdw 2.099 3.440 ... (remaining 55803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6963 Z= 0.280 Angle : 1.036 11.464 9536 Z= 0.579 Chirality : 0.061 0.281 1044 Planarity : 0.006 0.046 1090 Dihedral : 15.776 120.385 2738 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.48 % Rotamer: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.83 (0.25), residues: 743 helix: -2.62 (0.26), residues: 197 sheet: -2.85 (0.36), residues: 147 loop : -2.34 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 158 TYR 0.026 0.003 TYR A 238 PHE 0.030 0.004 PHE A 154 TRP 0.034 0.004 TRP A 623 HIS 0.004 0.002 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 6963) covalent geometry : angle 1.03604 ( 9536) hydrogen bonds : bond 0.20549 ( 241) hydrogen bonds : angle 9.69942 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8179 (mmt) cc_final: 0.7571 (mmt) REVERT: A 294 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8808 (mmmt) REVERT: A 480 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8751 (pttp) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.0881 time to fit residues: 15.5256 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 240 ASN A 288 ASN A 473 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096956 restraints weight = 20728.711| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 5.40 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6963 Z= 0.158 Angle : 0.702 9.952 9536 Z= 0.380 Chirality : 0.047 0.244 1044 Planarity : 0.004 0.037 1090 Dihedral : 18.752 123.448 1199 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.25 % Allowed : 8.98 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.57 (0.28), residues: 743 helix: -1.11 (0.32), residues: 222 sheet: -2.10 (0.45), residues: 122 loop : -1.91 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.027 0.002 TYR A 408 PHE 0.024 0.002 PHE A 591 TRP 0.044 0.004 TRP A 623 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6963) covalent geometry : angle 0.70220 ( 9536) hydrogen bonds : bond 0.04657 ( 241) hydrogen bonds : angle 6.64383 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8409 (tt0) cc_final: 0.7777 (tm-30) REVERT: A 24 MET cc_start: 0.8814 (mtm) cc_final: 0.8442 (ptp) REVERT: A 98 MET cc_start: 0.7852 (mmt) cc_final: 0.7243 (mmt) REVERT: A 197 GLU cc_start: 0.8599 (tp30) cc_final: 0.8378 (tp30) REVERT: A 294 LYS cc_start: 0.9391 (mmmm) cc_final: 0.8969 (mmmt) REVERT: A 363 MET cc_start: 0.8722 (mmt) cc_final: 0.8281 (mmt) REVERT: A 480 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8750 (mtpp) REVERT: A 513 HIS cc_start: 0.7735 (m170) cc_final: 0.7444 (m170) REVERT: A 533 MET cc_start: 0.8145 (mmm) cc_final: 0.7633 (mmm) REVERT: A 601 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8468 (mm-30) REVERT: A 646 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8577 (tm) outliers start: 15 outliers final: 5 residues processed: 112 average time/residue: 0.0804 time to fit residues: 12.3609 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 741 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 = 0.4078 r_free = 0.4078 target = 0.109195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.086489 restraints weight = 22013.121| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 5.26 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6963 Z= 0.218 Angle : 0.709 12.017 9536 Z= 0.379 Chirality : 0.046 0.158 1044 Planarity : 0.004 0.049 1090 Dihedral : 18.558 126.147 1199 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.69 % Allowed : 11.83 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.15 (0.29), residues: 743 helix: -0.81 (0.32), residues: 223 sheet: -1.90 (0.45), residues: 129 loop : -1.59 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.030 0.002 TYR A 238 PHE 0.026 0.003 PHE A 154 TRP 0.029 0.003 TRP A 623 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6963) covalent geometry : angle 0.70892 ( 9536) hydrogen bonds : bond 0.04282 ( 241) hydrogen bonds : angle 6.39533 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9017 (mtm) cc_final: 0.8514 (ptp) REVERT: A 98 MET cc_start: 0.8070 (mmt) cc_final: 0.7489 (mmt) REVERT: A 169 MET cc_start: 0.9090 (mmm) cc_final: 0.8637 (tpp) REVERT: A 295 GLU cc_start: 0.9330 (tp30) cc_final: 0.9129 (tp30) REVERT: A 363 MET cc_start: 0.8775 (mmt) cc_final: 0.8103 (mmm) REVERT: A 480 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8837 (mtpp) REVERT: A 513 HIS cc_start: 0.7786 (m170) cc_final: 0.7330 (m170) REVERT: A 533 MET cc_start: 0.8200 (mmm) cc_final: 0.7829 (mmm) REVERT: A 567 LEU cc_start: 0.8943 (tt) cc_final: 0.8720 (tt) REVERT: A 646 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8664 (tm) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.0738 time to fit residues: 10.3136 Evaluate side-chains 86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.4247 r_free = 0.4247 target = 0.121571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.097349 restraints weight = 20818.716| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 5.45 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6963 Z= 0.146 Angle : 0.644 8.166 9536 Z= 0.345 Chirality : 0.045 0.185 1044 Planarity : 0.004 0.046 1090 Dihedral : 18.355 123.793 1199 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.99 % Allowed : 11.68 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.84 (0.29), residues: 743 helix: -0.64 (0.33), residues: 225 sheet: -1.78 (0.46), residues: 128 loop : -1.31 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.028 0.001 TYR A 238 PHE 0.025 0.002 PHE A 147 TRP 0.056 0.005 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6963) covalent geometry : angle 0.64447 ( 9536) hydrogen bonds : bond 0.03743 ( 241) hydrogen bonds : angle 5.99999 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8389 (tt0) cc_final: 0.7786 (tm-30) REVERT: A 24 MET cc_start: 0.9043 (mtm) cc_final: 0.8521 (ptp) REVERT: A 98 MET cc_start: 0.7979 (mmt) cc_final: 0.7390 (mmt) REVERT: A 169 MET cc_start: 0.9108 (mmm) cc_final: 0.8656 (tpp) REVERT: A 363 MET cc_start: 0.8817 (mmt) cc_final: 0.8081 (mmm) REVERT: A 498 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8669 (mm-30) REVERT: A 513 HIS cc_start: 0.7603 (m170) cc_final: 0.7119 (m170) REVERT: A 646 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8586 (tm) REVERT: A 734 LYS cc_start: 0.9258 (pttp) cc_final: 0.8883 (ptpt) outliers start: 20 outliers final: 13 residues processed: 109 average time/residue: 0.0666 time to fit residues: 10.1184 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 0.0000 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN ** A 741 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 = 0.4268 r_free = 0.4268 target = 0.123115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.099169 restraints weight = 20995.963| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 5.60 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6963 Z= 0.129 Angle : 0.650 9.474 9536 Z= 0.344 Chirality : 0.045 0.241 1044 Planarity : 0.004 0.037 1090 Dihedral : 18.195 122.191 1199 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.69 % Allowed : 14.07 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.71 (0.30), residues: 743 helix: -0.70 (0.33), residues: 226 sheet: -1.71 (0.45), residues: 128 loop : -1.11 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.031 0.001 TYR A 238 PHE 0.019 0.002 PHE A 591 TRP 0.071 0.005 TRP A 623 HIS 0.007 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6963) covalent geometry : angle 0.64965 ( 9536) hydrogen bonds : bond 0.03642 ( 241) hydrogen bonds : angle 5.83211 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8363 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 24 MET cc_start: 0.9041 (mtm) cc_final: 0.8438 (ptp) REVERT: A 58 LYS cc_start: 0.9319 (mmtp) cc_final: 0.9057 (mmmm) REVERT: A 98 MET cc_start: 0.7927 (mmt) cc_final: 0.7342 (mmt) REVERT: A 148 LYS cc_start: 0.8384 (tppt) cc_final: 0.8147 (tppt) REVERT: A 169 MET cc_start: 0.9183 (mmm) cc_final: 0.8694 (tpp) REVERT: A 294 LYS cc_start: 0.9382 (mmmm) cc_final: 0.8971 (mmmt) REVERT: A 363 MET cc_start: 0.8860 (mmt) cc_final: 0.8092 (mmm) REVERT: A 365 ILE cc_start: 0.8674 (pt) cc_final: 0.8375 (mm) REVERT: A 498 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8675 (mm-30) REVERT: A 513 HIS cc_start: 0.7630 (m170) cc_final: 0.7184 (m170) REVERT: A 567 LEU cc_start: 0.8852 (tt) cc_final: 0.8640 (tt) REVERT: A 646 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8491 (tm) REVERT: A 731 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9253 (mmtp) REVERT: A 734 LYS cc_start: 0.9158 (pttp) cc_final: 0.8732 (pttm) outliers start: 18 outliers final: 11 residues processed: 108 average time/residue: 0.0786 time to fit residues: 11.5798 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 741 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 = 0.4147 r_free = 0.4147 target = 0.112663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.090140 restraints weight = 22630.247| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 5.46 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6963 Z= 0.139 Angle : 0.638 7.408 9536 Z= 0.340 Chirality : 0.045 0.162 1044 Planarity : 0.004 0.033 1090 Dihedral : 18.127 122.432 1199 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.10 % Allowed : 16.17 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.58 (0.30), residues: 743 helix: -0.71 (0.32), residues: 228 sheet: -1.60 (0.45), residues: 128 loop : -0.96 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.030 0.001 TYR A 238 PHE 0.014 0.002 PHE A 147 TRP 0.088 0.007 TRP A 623 HIS 0.018 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6963) covalent geometry : angle 0.63801 ( 9536) hydrogen bonds : bond 0.03541 ( 241) hydrogen bonds : angle 5.69547 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8417 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 24 MET cc_start: 0.8958 (mtm) cc_final: 0.8730 (ptp) REVERT: A 98 MET cc_start: 0.7965 (mmt) cc_final: 0.7388 (mmt) REVERT: A 148 LYS cc_start: 0.8845 (tppt) cc_final: 0.8541 (tptp) REVERT: A 169 MET cc_start: 0.9137 (mmm) cc_final: 0.8650 (tpp) REVERT: A 294 LYS cc_start: 0.9413 (mmmm) cc_final: 0.8990 (mmmt) REVERT: A 363 MET cc_start: 0.8806 (mmt) cc_final: 0.8032 (mmm) REVERT: A 498 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8668 (mm-30) REVERT: A 513 HIS cc_start: 0.7571 (m170) cc_final: 0.7093 (m170) REVERT: A 646 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8624 (tm) REVERT: A 673 MET cc_start: 0.8094 (ttp) cc_final: 0.7889 (ttp) REVERT: A 731 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9190 (mmtp) REVERT: A 734 LYS cc_start: 0.9232 (pttp) cc_final: 0.8818 (pttm) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.0780 time to fit residues: 10.8650 Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 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 = 0.4100 r_free = 0.4100 target = 0.109537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086796 restraints weight = 22152.702| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 5.31 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6963 Z= 0.198 Angle : 0.677 6.742 9536 Z= 0.359 Chirality : 0.046 0.162 1044 Planarity : 0.004 0.040 1090 Dihedral : 18.156 123.665 1199 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.54 % Allowed : 16.02 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.52 (0.30), residues: 743 helix: -0.67 (0.33), residues: 228 sheet: -1.68 (0.47), residues: 125 loop : -0.88 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 56 TYR 0.029 0.002 TYR A 511 PHE 0.015 0.002 PHE A 591 TRP 0.070 0.005 TRP A 623 HIS 0.007 0.002 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 6963) covalent geometry : angle 0.67668 ( 9536) hydrogen bonds : bond 0.03730 ( 241) hydrogen bonds : angle 5.82997 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8377 (tt0) cc_final: 0.7961 (tm-30) REVERT: A 98 MET cc_start: 0.8099 (mmt) cc_final: 0.7561 (mmt) REVERT: A 148 LYS cc_start: 0.9064 (tppt) cc_final: 0.8818 (tptp) REVERT: A 169 MET cc_start: 0.9100 (mmm) cc_final: 0.8612 (tpp) REVERT: A 294 LYS cc_start: 0.9443 (mmmm) cc_final: 0.9008 (mmmt) REVERT: A 363 MET cc_start: 0.8774 (mmt) cc_final: 0.8189 (mmt) REVERT: A 498 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8714 (mm-30) REVERT: A 513 HIS cc_start: 0.7570 (m170) cc_final: 0.7118 (m170) REVERT: A 646 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8732 (tm) REVERT: A 731 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9169 (mmtp) REVERT: A 734 LYS cc_start: 0.9248 (pttp) cc_final: 0.8819 (pttp) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.0721 time to fit residues: 9.9022 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.108124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.085438 restraints weight = 22419.954| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 5.38 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6963 Z= 0.202 Angle : 0.697 12.324 9536 Z= 0.367 Chirality : 0.046 0.181 1044 Planarity : 0.004 0.055 1090 Dihedral : 18.221 123.836 1199 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 17.07 % Favored : 80.39 % 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: -1.59 (0.30), residues: 743 helix: -0.83 (0.32), residues: 229 sheet: -1.49 (0.49), residues: 121 loop : -0.94 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 158 TYR 0.032 0.002 TYR A 238 PHE 0.015 0.002 PHE A 591 TRP 0.067 0.005 TRP A 623 HIS 0.007 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6963) covalent geometry : angle 0.69704 ( 9536) hydrogen bonds : bond 0.03809 ( 241) hydrogen bonds : angle 5.95071 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8427 (tt0) cc_final: 0.7933 (tm-30) REVERT: A 98 MET cc_start: 0.8066 (mmt) cc_final: 0.7565 (mmt) REVERT: A 169 MET cc_start: 0.9103 (mmm) cc_final: 0.8622 (tpp) REVERT: A 294 LYS cc_start: 0.9421 (mmmm) cc_final: 0.8990 (mmmt) REVERT: A 363 MET cc_start: 0.8834 (mmt) cc_final: 0.8155 (mmt) REVERT: A 498 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8730 (mm-30) REVERT: A 513 HIS cc_start: 0.7582 (m170) cc_final: 0.7034 (m170) REVERT: A 533 MET cc_start: 0.7988 (mmm) cc_final: 0.7686 (mmm) REVERT: A 646 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8801 (tm) REVERT: A 731 LYS cc_start: 0.9517 (mmmm) cc_final: 0.9196 (mmtp) REVERT: A 734 LYS cc_start: 0.9290 (pttp) cc_final: 0.8904 (pttp) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 0.0698 time to fit residues: 9.7066 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 64.9189 > 50: distance: 4 - 9: 34.022 distance: 9 - 10: 45.828 distance: 10 - 11: 17.852 distance: 10 - 13: 11.942 distance: 11 - 12: 47.789 distance: 11 - 18: 18.153 distance: 15 - 16: 21.720 distance: 15 - 17: 17.188 distance: 18 - 138: 35.232 distance: 20 - 21: 16.702 distance: 22 - 23: 30.899 distance: 22 - 170: 35.334 distance: 23 - 24: 29.702 distance: 23 - 26: 31.661 distance: 24 - 25: 3.382 distance: 24 - 30: 42.990 distance: 25 - 167: 27.795 distance: 26 - 27: 6.690 distance: 26 - 28: 9.096 distance: 27 - 29: 6.632 distance: 31 - 32: 33.592 distance: 32 - 33: 17.898 distance: 32 - 34: 38.306 distance: 34 - 35: 25.041 distance: 40 - 41: 37.235 distance: 41 - 42: 4.968 distance: 41 - 44: 36.575 distance: 42 - 43: 39.055 distance: 42 - 47: 45.943 distance: 44 - 45: 28.420 distance: 44 - 46: 15.948 distance: 47 - 48: 17.704 distance: 48 - 49: 39.643 distance: 48 - 51: 12.807 distance: 49 - 55: 38.916 distance: 51 - 52: 33.147 distance: 52 - 53: 39.080 distance: 52 - 54: 12.396 distance: 55 - 56: 31.477 distance: 55 - 61: 55.446 distance: 56 - 57: 24.196 distance: 56 - 59: 10.674 distance: 57 - 58: 21.616 distance: 57 - 62: 20.699 distance: 59 - 60: 17.540 distance: 60 - 61: 43.018 distance: 63 - 64: 10.746 distance: 63 - 66: 39.040 distance: 64 - 65: 12.827 distance: 64 - 70: 27.644 distance: 66 - 67: 42.270 distance: 67 - 68: 48.402 distance: 68 - 69: 49.291 distance: 70 - 71: 28.475 distance: 71 - 72: 49.077 distance: 71 - 74: 12.173 distance: 72 - 73: 4.904 distance: 72 - 78: 32.219 distance: 74 - 75: 41.011 distance: 75 - 77: 40.835