Starting phenix.real_space_refine on Sun May 11 04:07:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.map" model { file = "/net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w4o_37267/05_2025/8w4o_37267.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 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 P 3 5.49 5 Mg 36 5.21 5 S 10 5.16 5 C 4356 2.51 5 N 763 2.21 5 O 878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6046 Number of models: 1 Model: "" Number of chains: 6 Chain: "5" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1280 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 156} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "7" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1222 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 154} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "6" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1209 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 51 Chain: "5" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 914 Unusual residues: {'A86': 3, 'CLA': 11, 'ET4': 1, 'LHG': 3, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-3': 2, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 58 Chain: "7" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 707 Unusual residues: {'A86': 2, 'CLA': 12, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 4, 'CLA:plan-4': 7, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 84 Chain: "6" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 714 Unusual residues: {'A86': 1, 'CLA': 13, 'DD6': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 5.99, per 1000 atoms: 0.99 Number of scatterers: 6046 At special positions: 0 Unit cell: (80.56, 113.42, 66.78, 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) S 10 16.00 P 3 15.00 Mg 36 11.99 O 878 8.00 N 763 7.00 C 4356 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 459.9 milliseconds 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 57.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain '5' and resid 61 through 95 removed outlier: 3.589A pdb=" N SER 5 66 " --> pdb=" O PRO 5 62 " (cutoff:3.500A) Proline residue: 5 89 - end of helix Processing helix chain '5' and resid 108 through 112 removed outlier: 3.570A pdb=" N VAL 5 112 " --> pdb=" O ALA 5 109 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 138 removed outlier: 3.819A pdb=" N LEU 5 120 " --> pdb=" O ASP 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 158 through 189 Processing helix chain '5' and resid 192 through 199 Processing helix chain '5' and resid 200 through 202 No H-bonds generated for 'chain '5' and resid 200 through 202' Processing helix chain '7' and resid 46 through 71 Processing helix chain '7' and resid 72 through 76 Processing helix chain '7' and resid 103 through 119 removed outlier: 3.638A pdb=" N LEU 7 113 " --> pdb=" O GLN 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 126 through 130 Processing helix chain '7' and resid 139 through 168 removed outlier: 3.649A pdb=" N LEU 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 181 through 185 Processing helix chain '6' and resid 59 through 86 Processing helix chain '6' and resid 87 through 89 No H-bonds generated for 'chain '6' and resid 87 through 89' Processing helix chain '6' and resid 116 through 132 Processing helix chain '6' and resid 139 through 143 Processing helix chain '6' and resid 149 through 181 Processing helix chain '6' and resid 194 through 198 213 hydrogen bonds defined for protein. 606 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: 1.33 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.35: 1498 1.35 - 1.54: 4642 1.54 - 1.72: 152 1.72 - 1.91: 17 1.91 - 2.09: 144 Bond restraints: 6453 Sorted by residual: bond pdb=" C30 DD6 6 204 " pdb=" C31 DD6 6 204 " ideal model delta sigma weight residual 1.421 1.242 0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C27 DD6 6 204 " pdb=" C29 DD6 6 204 " ideal model delta sigma weight residual 1.418 1.242 0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C30 DD6 7 304 " pdb=" C31 DD6 7 304 " ideal model delta sigma weight residual 1.421 1.252 0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C27 DD6 7 304 " pdb=" C29 DD6 7 304 " ideal model delta sigma weight residual 1.418 1.253 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C30 DD6 6 203 " pdb=" C31 DD6 6 203 " ideal model delta sigma weight residual 1.421 1.259 0.162 2.00e-02 2.50e+03 6.52e+01 ... (remaining 6448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.88: 9243 5.88 - 11.76: 169 11.76 - 17.63: 13 17.63 - 23.51: 0 23.51 - 29.39: 5 Bond angle restraints: 9430 Sorted by residual: angle pdb=" C14 A86 7 302 " pdb=" C15 A86 7 302 " pdb=" O1 A86 7 302 " ideal model delta sigma weight residual 115.67 86.28 29.39 3.00e+00 1.11e-01 9.60e+01 angle pdb=" C14 A86 7 301 " pdb=" C15 A86 7 301 " pdb=" O1 A86 7 301 " ideal model delta sigma weight residual 115.67 88.91 26.76 3.00e+00 1.11e-01 7.96e+01 angle pdb=" C14 A86 5 320 " pdb=" C15 A86 5 320 " pdb=" O1 A86 5 320 " ideal model delta sigma weight residual 115.67 89.12 26.55 3.00e+00 1.11e-01 7.83e+01 angle pdb=" C14 A86 6 202 " pdb=" C15 A86 6 202 " pdb=" O1 A86 6 202 " ideal model delta sigma weight residual 115.67 90.63 25.04 3.00e+00 1.11e-01 6.97e+01 angle pdb=" C14 A86 5 301 " pdb=" C15 A86 5 301 " pdb=" C20 A86 5 301 " ideal model delta sigma weight residual 117.95 93.30 24.65 3.00e+00 1.11e-01 6.75e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 2753 35.43 - 70.87: 225 70.87 - 106.30: 72 106.30 - 141.74: 32 141.74 - 177.17: 14 Dihedral angle restraints: 3096 sinusoidal: 1697 harmonic: 1399 Sorted by residual: dihedral pdb=" C34 A86 5 303 " pdb=" C38 A86 5 303 " pdb=" O4 A86 5 303 " pdb=" C39 A86 5 303 " ideal model delta sinusoidal sigma weight residual -177.27 -0.10 -177.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 ET4 5 302 " pdb=" C23 ET4 5 302 " pdb=" C32 ET4 5 302 " pdb=" C33 ET4 5 302 " ideal model delta sinusoidal sigma weight residual 170.20 -16.65 -173.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C34 A86 7 302 " pdb=" C38 A86 7 302 " pdb=" O4 A86 7 302 " pdb=" C39 A86 7 302 " ideal model delta sinusoidal sigma weight residual -177.27 -6.51 -170.76 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.275: 747 0.275 - 0.550: 12 0.550 - 0.825: 1 0.825 - 1.100: 2 1.100 - 1.375: 1 Chirality restraints: 763 Sorted by residual: chirality pdb=" C15 A86 5 301 " pdb=" C14 A86 5 301 " pdb=" C16 A86 5 301 " pdb=" C20 A86 5 301 " both_signs ideal model delta sigma weight residual True 1.20 2.58 -1.37 2.00e-01 2.50e+01 4.73e+01 chirality pdb=" C20 A86 5 303 " pdb=" C15 A86 5 303 " pdb=" C19 A86 5 303 " pdb=" C21 A86 5 303 " both_signs ideal model delta sigma weight residual True 1.08 0.12 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" C15 A86 5 303 " pdb=" C14 A86 5 303 " pdb=" C16 A86 5 303 " pdb=" C20 A86 5 303 " both_signs ideal model delta sigma weight residual True 1.20 0.35 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 760 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG 5 317 " 0.099 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C8 LHG 5 317 " -0.029 2.00e-02 2.50e+03 pdb=" O7 LHG 5 317 " -0.031 2.00e-02 2.50e+03 pdb=" O9 LHG 5 317 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG 5 318 " 0.082 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C24 LHG 5 318 " -0.025 2.00e-02 2.50e+03 pdb=" O10 LHG 5 318 " -0.030 2.00e-02 2.50e+03 pdb=" O8 LHG 5 318 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 SQD 5 319 " -0.076 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C24 SQD 5 319 " 0.023 2.00e-02 2.50e+03 pdb=" O10 SQD 5 319 " 0.029 2.00e-02 2.50e+03 pdb=" O48 SQD 5 319 " 0.024 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 905 2.77 - 3.30: 5388 3.30 - 3.83: 10499 3.83 - 4.37: 11702 4.37 - 4.90: 19387 Nonbonded interactions: 47881 Sorted by model distance: nonbonded pdb=" O ASP 5 199 " pdb=" OG SER 5 200 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU 6 70 " pdb=" NE ARG 6 162 " model vdw 2.268 3.120 nonbonded pdb=" OD2 ASP 7 37 " pdb=" OG SER 7 42 " model vdw 2.277 3.040 nonbonded pdb=" O ALA 5 125 " pdb=" OG SER 5 128 " model vdw 2.302 3.040 nonbonded pdb=" O PHE 6 184 " pdb=" O4 SQD 5 319 " model vdw 2.305 3.040 ... (remaining 47876 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: 15.330 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.090 Find NCS groups from input model: 0.070 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.040 0.887 6475 Z= 2.038 Angle : 1.697 29.389 9430 Z= 0.623 Chirality : 0.099 1.375 763 Planarity : 0.007 0.091 1276 Dihedral : 31.536 177.169 2206 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.85 % Favored : 85.95 % Rotamer: Outliers : 0.87 % Allowed : 0.87 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.38), residues: 491 helix: 0.31 (0.32), residues: 263 sheet: None (None), residues: 0 loop : -4.38 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 92 HIS 0.004 0.001 HIS 7 60 PHE 0.013 0.001 PHE 6 136 TYR 0.010 0.001 TYR 6 84 ARG 0.003 0.001 ARG 6 133 Details of bonding type rmsd hydrogen bonds : bond 0.11881 ( 213) hydrogen bonds : angle 5.06091 ( 606) covalent geometry : bond 0.01138 ( 6453) covalent geometry : angle 1.69666 ( 9430) Misc. bond : bond 0.65316 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.457 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.1426 time to fit residues: 17.4269 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 80 GLN 7 109 GLN 7 164 GLN 6 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065797 restraints weight = 13520.402| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.89 r_work: 0.2651 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.045 2.298 6475 Z= 4.370 Angle : 0.870 11.639 9430 Z= 0.348 Chirality : 0.083 0.982 763 Planarity : 0.006 0.071 1276 Dihedral : 30.661 177.616 1439 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.35 % Favored : 91.24 % Rotamer: Outliers : 2.60 % Allowed : 11.56 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.38), residues: 491 helix: 1.19 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.51 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 135 HIS 0.005 0.002 HIS 5 75 PHE 0.011 0.001 PHE 6 125 TYR 0.012 0.001 TYR 7 77 ARG 0.004 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05911 ( 213) hydrogen bonds : angle 3.77392 ( 606) covalent geometry : bond 0.00432 ( 6453) covalent geometry : angle 0.87018 ( 9430) Misc. bond : bond 0.77545 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8107 (t80) REVERT: 6 107 ASN cc_start: 0.8696 (t0) cc_final: 0.8267 (t0) REVERT: 6 168 ILE cc_start: 0.9270 (tp) cc_final: 0.9013 (tp) REVERT: 6 175 ASP cc_start: 0.8761 (t0) cc_final: 0.8372 (t0) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1545 time to fit residues: 18.1179 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3002 r_free = 0.3002 target = 0.076826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.065301 restraints weight = 13715.536| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.91 r_work: 0.2638 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.473 6475 Z= 0.206 Angle : 0.816 12.195 9430 Z= 0.331 Chirality : 0.077 0.898 763 Planarity : 0.006 0.059 1276 Dihedral : 29.554 174.462 1439 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.55 % Favored : 91.24 % Rotamer: Outliers : 2.60 % Allowed : 14.16 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.39), residues: 491 helix: 1.50 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.31 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.010 0.001 PHE 6 125 TYR 0.015 0.001 TYR 7 77 ARG 0.006 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05875 ( 213) hydrogen bonds : angle 3.71559 ( 606) covalent geometry : bond 0.00434 ( 6453) covalent geometry : angle 0.81616 ( 9430) Misc. bond : bond 0.19872 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8295 (t80) REVERT: 6 107 ASN cc_start: 0.8748 (t0) cc_final: 0.8420 (t0) REVERT: 6 168 ILE cc_start: 0.9245 (tp) cc_final: 0.8940 (tp) REVERT: 6 175 ASP cc_start: 0.8763 (t0) cc_final: 0.8353 (t0) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1422 time to fit residues: 14.7580 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 7 residue 163 SER Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 0.0570 chunk 39 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 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 = 0.3015 r_free = 0.3015 target = 0.077525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.065953 restraints weight = 13767.211| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.93 r_work: 0.2651 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.465 6475 Z= 0.159 Angle : 0.791 12.033 9430 Z= 0.326 Chirality : 0.077 0.914 763 Planarity : 0.005 0.055 1276 Dihedral : 29.157 172.074 1439 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 2.89 % Allowed : 13.58 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.39), residues: 491 helix: 1.67 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.22 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.008 0.001 PHE 6 125 TYR 0.011 0.001 TYR 5 94 ARG 0.007 0.000 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 213) hydrogen bonds : angle 3.57579 ( 606) covalent geometry : bond 0.00315 ( 6453) covalent geometry : angle 0.79129 ( 9430) Misc. bond : bond 0.19304 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8348 (t80) REVERT: 6 107 ASN cc_start: 0.8711 (t0) cc_final: 0.8337 (t0) REVERT: 6 168 ILE cc_start: 0.9239 (tp) cc_final: 0.8938 (tp) REVERT: 6 175 ASP cc_start: 0.8758 (t0) cc_final: 0.8342 (t0) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.1349 time to fit residues: 14.0773 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 91 ASP Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.065579 restraints weight = 13685.513| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.93 r_work: 0.2647 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.738 6475 Z= 2.175 Angle : 0.776 12.047 9430 Z= 0.318 Chirality : 0.077 0.911 763 Planarity : 0.005 0.050 1276 Dihedral : 28.809 169.190 1439 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.96 % Favored : 90.84 % Rotamer: Outliers : 3.18 % Allowed : 13.87 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.39), residues: 491 helix: 1.82 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.14 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.014 0.001 TYR 5 94 ARG 0.008 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05656 ( 213) hydrogen bonds : angle 3.53314 ( 606) covalent geometry : bond 0.00362 ( 6453) covalent geometry : angle 0.77630 ( 9430) Misc. bond : bond 0.52010 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.537 Fit side-chains REVERT: 6 84 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8389 (t80) REVERT: 6 107 ASN cc_start: 0.8718 (t0) cc_final: 0.8350 (t0) REVERT: 6 168 ILE cc_start: 0.9238 (tp) cc_final: 0.8926 (tp) REVERT: 6 175 ASP cc_start: 0.8751 (t0) cc_final: 0.8318 (t0) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.1349 time to fit residues: 14.5379 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 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 = 0.3006 r_free = 0.3006 target = 0.076923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.065521 restraints weight = 13538.783| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.89 r_work: 0.2654 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 1.418 6475 Z= 0.242 Angle : 0.772 12.002 9430 Z= 0.317 Chirality : 0.077 0.915 763 Planarity : 0.005 0.047 1276 Dihedral : 28.702 168.000 1439 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 2.89 % Allowed : 15.61 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.39), residues: 491 helix: 1.83 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.10 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 92 HIS 0.004 0.001 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 5 94 ARG 0.008 0.001 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05535 ( 213) hydrogen bonds : angle 3.53085 ( 606) covalent geometry : bond 0.00341 ( 6453) covalent geometry : angle 0.77172 ( 9430) Misc. bond : bond 0.35570 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8407 (t80) REVERT: 6 107 ASN cc_start: 0.8721 (t0) cc_final: 0.8436 (t0) REVERT: 6 168 ILE cc_start: 0.9243 (tp) cc_final: 0.8931 (tp) REVERT: 6 175 ASP cc_start: 0.8755 (t0) cc_final: 0.8320 (t0) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.1355 time to fit residues: 14.1557 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 138 ASN Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.0070 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3014 r_free = 0.3014 target = 0.077362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.065899 restraints weight = 13511.418| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.91 r_work: 0.2661 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 1.341 6475 Z= 0.222 Angle : 0.753 11.974 9430 Z= 0.308 Chirality : 0.077 0.922 763 Planarity : 0.005 0.045 1276 Dihedral : 28.578 166.525 1439 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 3.18 % Allowed : 15.61 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 491 helix: 1.89 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.07 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 5 94 ARG 0.008 0.000 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 213) hydrogen bonds : angle 3.51180 ( 606) covalent geometry : bond 0.00290 ( 6453) covalent geometry : angle 0.75312 ( 9430) Misc. bond : bond 0.34211 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8401 (t80) REVERT: 6 107 ASN cc_start: 0.8707 (t0) cc_final: 0.8431 (t0) REVERT: 6 168 ILE cc_start: 0.9225 (tp) cc_final: 0.8916 (tp) REVERT: 6 175 ASP cc_start: 0.8733 (t0) cc_final: 0.8293 (t0) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1326 time to fit residues: 13.9996 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.0670 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3020 r_free = 0.3020 target = 0.077638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.066239 restraints weight = 13576.074| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.90 r_work: 0.2663 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.341 6475 Z= 0.798 Angle : 0.753 11.974 9430 Z= 0.308 Chirality : 0.077 0.922 763 Planarity : 0.005 0.045 1276 Dihedral : 28.578 166.525 1439 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 491 helix: 1.89 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.07 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 5 94 ARG 0.008 0.000 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 213) hydrogen bonds : angle 3.51180 ( 606) covalent geometry : bond 0.00290 ( 6453) covalent geometry : angle 0.75317 ( 9430) Misc. bond : bond 0.36649 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8403 (t80) REVERT: 6 107 ASN cc_start: 0.8703 (t0) cc_final: 0.8429 (t0) REVERT: 6 168 ILE cc_start: 0.9227 (tp) cc_final: 0.8918 (tp) REVERT: 6 175 ASP cc_start: 0.8734 (t0) cc_final: 0.8293 (t0) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.1373 time to fit residues: 14.2441 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 0.0010 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 122 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 = 0.3021 r_free = 0.3021 target = 0.077803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.066320 restraints weight = 13569.857| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.91 r_work: 0.2662 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.341 6475 Z= 0.897 Angle : 0.753 11.974 9430 Z= 0.308 Chirality : 0.077 0.922 763 Planarity : 0.005 0.045 1276 Dihedral : 28.578 166.525 1439 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.76 % Favored : 91.04 % Rotamer: Outliers : 2.60 % Allowed : 16.76 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 491 helix: 1.89 (0.30), residues: 267 sheet: None (None), residues: 0 loop : -3.07 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 92 HIS 0.003 0.001 HIS 6 73 PHE 0.009 0.001 PHE 6 125 TYR 0.012 0.001 TYR 5 94 ARG 0.008 0.000 ARG 6 91 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 213) hydrogen bonds : angle 3.51180 ( 606) covalent geometry : bond 0.00290 ( 6453) covalent geometry : angle 0.75317 ( 9430) Misc. bond : bond 0.37317 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 982 Ramachandran restraints generated. 491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: 6 84 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8403 (t80) REVERT: 6 107 ASN cc_start: 0.8703 (t0) cc_final: 0.8429 (t0) REVERT: 6 168 ILE cc_start: 0.9227 (tp) cc_final: 0.8918 (tp) REVERT: 6 175 ASP cc_start: 0.8735 (t0) cc_final: 0.8294 (t0) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1341 time to fit residues: 13.8328 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 42 VAL Chi-restraints excluded: chain 5 residue 128 SER Chi-restraints excluded: chain 5 residue 185 GLN Chi-restraints excluded: chain 7 residue 139 GLU Chi-restraints excluded: chain 6 residue 84 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 ILE Chi-restraints excluded: chain 6 residue 169 LEU Chi-restraints excluded: chain 6 residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.3213 > 50: distance: 41 - 45: 8.062 distance: 45 - 46: 7.255 distance: 46 - 47: 8.806 distance: 46 - 49: 7.558 distance: 47 - 48: 15.904 distance: 47 - 53: 11.257 distance: 49 - 50: 4.825 distance: 49 - 51: 5.509 distance: 50 - 52: 8.786 distance: 53 - 54: 6.623 distance: 54 - 55: 11.962 distance: 55 - 56: 3.242 distance: 55 - 60: 5.539 distance: 57 - 58: 4.676 distance: 60 - 61: 3.767 distance: 61 - 62: 4.130 distance: 61 - 64: 4.687 distance: 62 - 63: 24.477 distance: 62 - 68: 18.999 distance: 64 - 65: 5.912 distance: 65 - 66: 3.945 distance: 65 - 67: 23.143 distance: 68 - 69: 12.999 distance: 69 - 70: 26.487 distance: 70 - 71: 10.797 distance: 70 - 72: 18.212 distance: 72 - 73: 9.256 distance: 73 - 74: 10.310 distance: 73 - 76: 13.344 distance: 74 - 75: 12.987 distance: 74 - 79: 13.215 distance: 76 - 77: 9.447 distance: 79 - 80: 5.413 distance: 80 - 81: 8.085 distance: 80 - 83: 14.136 distance: 81 - 82: 6.260 distance: 81 - 84: 4.707 distance: 84 - 85: 4.736 distance: 85 - 86: 8.300 distance: 85 - 88: 11.129 distance: 86 - 87: 20.420 distance: 86 - 89: 6.171 distance: 89 - 90: 7.346 distance: 90 - 91: 7.290 distance: 90 - 93: 5.270 distance: 91 - 92: 3.053 distance: 91 - 97: 9.919 distance: 93 - 94: 6.388 distance: 93 - 95: 7.808 distance: 94 - 96: 6.307 distance: 97 - 98: 9.621 distance: 98 - 101: 9.745 distance: 99 - 100: 3.166 distance: 99 - 102: 5.781 distance: 103 - 104: 3.920 distance: 103 - 106: 4.013 distance: 104 - 105: 3.151 distance: 106 - 107: 3.784 distance: 107 - 108: 3.911 distance: 109 - 111: 3.562 distance: 112 - 113: 4.438