Starting phenix.real_space_refine on Wed Jul 1 21:40:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exa_31367/07_2026/7exa_31367.map" } resolution = 2.9 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= 0.007 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 1942 2.51 5 N 530 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 0.96, per 1000 atoms: 0.31 Number of scatterers: 3088 At special positions: 0 Unit cell: (91.74, 66.66, 79.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 591 8.00 N 530 7.00 C 1942 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: 0.26 Conformation dependent library (CDL) restraints added in 127.3 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 69.5% alpha, 3.7% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.289A pdb=" N LEU A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.553A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 179 removed outlier: 3.582A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 4.202A pdb=" N ASP A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.639A pdb=" N SER A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 262 removed outlier: 3.655A pdb=" N MET A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.770A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.653A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 358 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.275A pdb=" N VAL A 35 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS A 102 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 37 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 39 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY A 106 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 115 " --> pdb=" O ASP A 105 " (cutoff:3.500A) 167 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.35 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: 697 1.33 - 1.45: 697 1.45 - 1.57: 1725 1.57 - 1.69: 11 1.69 - 1.81: 31 Bond restraints: 3161 Sorted by residual: bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" N GLN A 187 " pdb=" CA GLN A 187 " ideal model delta sigma weight residual 1.455 1.489 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.01e-02 9.80e+03 1.18e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.99e+00 bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.56e+00 ... (remaining 3156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 3694 1.77 - 3.53: 545 3.53 - 5.30: 56 5.30 - 7.07: 5 7.07 - 8.83: 4 Bond angle restraints: 4304 Sorted by residual: angle pdb=" C4' U B 23 " pdb=" C3' U B 23 " pdb=" O3' U B 23 " ideal model delta sigma weight residual 113.00 121.83 -8.83 1.50e+00 4.44e-01 3.47e+01 angle pdb=" C4' U B 24 " pdb=" C3' U B 24 " pdb=" O3' U B 24 " ideal model delta sigma weight residual 113.00 121.10 -8.10 1.50e+00 4.44e-01 2.91e+01 angle pdb=" C4' U B 20 " pdb=" C3' U B 20 " pdb=" O3' U B 20 " ideal model delta sigma weight residual 113.00 120.61 -7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" O GLY A 244 " ideal model delta sigma weight residual 122.28 118.38 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" O2' U B 20 " pdb=" C2' U B 20 " pdb=" C1' U B 20 " ideal model delta sigma weight residual 108.40 102.64 5.76 1.50e+00 4.44e-01 1.47e+01 ... (remaining 4299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1688 17.89 - 35.79: 185 35.79 - 53.68: 40 53.68 - 71.58: 13 71.58 - 89.47: 5 Dihedral angle restraints: 1931 sinusoidal: 839 harmonic: 1092 Sorted by residual: dihedral pdb=" C5' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" O3' U B 25 " ideal model delta sinusoidal sigma weight residual 147.00 106.23 40.77 1 8.00e+00 1.56e-02 3.64e+01 dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual -35.00 0.49 -35.49 1 8.00e+00 1.56e-02 2.79e+01 dihedral pdb=" O4' U B 25 " pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " ideal model delta sinusoidal sigma weight residual 24.00 -11.43 35.43 1 8.00e+00 1.56e-02 2.78e+01 ... (remaining 1928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 294 0.052 - 0.105: 120 0.105 - 0.157: 40 0.157 - 0.209: 14 0.209 - 0.261: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA LEU A 90 " pdb=" N LEU A 90 " pdb=" C LEU A 90 " pdb=" CB LEU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' U B 23 " pdb=" C4' U B 23 " pdb=" O3' U B 23 " pdb=" C2' U B 23 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 477 not shown) Planarity restraints: 543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 277 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C LEU A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU A 277 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 24 " -0.020 2.00e-02 2.50e+03 1.21e-02 3.30e+00 pdb=" N1 U B 24 " 0.030 2.00e-02 2.50e+03 pdb=" C2 U B 24 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U B 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 24 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U B 24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 314 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C ALA A 314 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 314 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 315 " -0.010 2.00e-02 2.50e+03 ... (remaining 540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 16 2.57 - 3.15: 2400 3.15 - 3.73: 4705 3.73 - 4.32: 6964 4.32 - 4.90: 11041 Nonbonded interactions: 25126 Sorted by model distance: nonbonded pdb=" O LYS A 180 " pdb=" O ALA A 184 " model vdw 1.984 3.040 nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLN A 231 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 61 " pdb=" NH2 ARG A 69 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" OD2 ASP A 136 " model vdw 2.385 3.040 nonbonded pdb=" O ALA A 64 " pdb=" NH1 ARG A 69 " model vdw 2.394 3.120 ... (remaining 25121 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: 10.760 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.910 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.010 0.042 3161 Z= 0.692 Angle : 1.219 8.833 4304 Z= 0.894 Chirality : 0.074 0.261 480 Planarity : 0.005 0.030 543 Dihedral : 16.181 89.470 1233 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 9.94 % Favored : 88.46 % 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 are not related in a simple way. whole: -0.45 (0.40), residues: 372 helix: -0.46 (0.31), residues: 223 sheet: 0.89 (1.43), residues: 14 loop : 0.20 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 10 TYR 0.022 0.003 TYR A 361 PHE 0.016 0.003 PHE A 289 TRP 0.011 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01040 / 0.69 ( 3161) covalent geometry : angle 1.21858 / 0.89 ( 4304) hydrogen bonds : bond 0.18406 / 11.63 ( 167) hydrogen bonds : angle 6.19003 / 4.44 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.074 Fit side-chains REVERT: A 6 LYS cc_start: 0.8325 (mttt) cc_final: 0.8024 (mttp) REVERT: A 65 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7552 (mtp180) REVERT: A 88 ILE cc_start: 0.7996 (mm) cc_final: 0.7723 (mm) REVERT: A 214 GLU cc_start: 0.6853 (mp0) cc_final: 0.6228 (mm-30) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.7494 time to fit residues: 46.5521 Evaluate side-chains 43 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 248 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 63 ASN A 68 HIS A 121 ASN A 212 GLN A 238 GLN A 346 GLN A 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.130238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.109540 restraints weight = 3053.731| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.00 r_work: 0.2848 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3161 Z= 0.156 Angle : 0.575 5.633 4304 Z= 0.308 Chirality : 0.042 0.203 480 Planarity : 0.004 0.034 543 Dihedral : 9.794 60.570 521 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.56 % Allowed : 13.14 % Favored : 84.29 % 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 are not related in a simple way. whole: 1.73 (0.44), residues: 372 helix: 1.36 (0.35), residues: 220 sheet: 1.42 (1.44), residues: 14 loop : 1.01 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.017 0.002 TYR A 361 PHE 0.013 0.002 PHE A 289 TRP 0.008 0.002 TRP A 175 HIS 0.003 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 3161) covalent geometry : angle 0.57529 / 0.31 ( 4304) hydrogen bonds : bond 0.05591 / 3.49 ( 167) hydrogen bonds : angle 4.57833 / 3.24 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.118 Fit side-chains REVERT: A 6 LYS cc_start: 0.8542 (mttt) cc_final: 0.8249 (mttt) REVERT: A 17 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (mm) REVERT: A 62 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7523 (mt0) REVERT: A 208 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7144 (ttp-170) REVERT: A 214 GLU cc_start: 0.7013 (mp0) cc_final: 0.6440 (tp30) outliers start: 8 outliers final: 1 residues processed: 50 average time/residue: 0.7366 time to fit residues: 37.5614 Evaluate side-chains 44 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.108790 restraints weight = 3079.538| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.06 r_work: 0.2836 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.142 Angle : 0.535 4.965 4304 Z= 0.282 Chirality : 0.041 0.191 480 Planarity : 0.004 0.033 543 Dihedral : 9.262 60.443 516 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.53 % Allowed : 12.18 % Favored : 84.29 % 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 are not related in a simple way. whole: 2.00 (0.44), residues: 372 helix: 1.66 (0.36), residues: 220 sheet: 1.88 (1.46), residues: 14 loop : 0.91 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.017 0.002 TYR A 361 PHE 0.012 0.002 PHE A 289 TRP 0.007 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3161) covalent geometry : angle 0.53527 / 0.28 ( 4304) hydrogen bonds : bond 0.05228 / 3.22 ( 167) hydrogen bonds : angle 4.31464 / 3.04 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.075 Fit side-chains REVERT: A 6 LYS cc_start: 0.8513 (mttt) cc_final: 0.8246 (mttt) REVERT: A 93 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7468 (mtm180) REVERT: A 208 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7184 (ttp-170) REVERT: A 214 GLU cc_start: 0.6993 (mp0) cc_final: 0.6441 (tp30) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.7775 time to fit residues: 45.1895 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.131777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.111020 restraints weight = 3092.774| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 0.99 r_work: 0.2847 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3161 Z= 0.119 Angle : 0.489 4.717 4304 Z= 0.260 Chirality : 0.039 0.191 480 Planarity : 0.004 0.032 543 Dihedral : 9.060 60.423 516 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.53 % Allowed : 12.82 % Favored : 83.65 % 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 are not related in a simple way. whole: 2.19 (0.43), residues: 372 helix: 1.85 (0.36), residues: 220 sheet: 2.18 (1.51), residues: 14 loop : 0.88 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.015 0.001 TYR A 361 PHE 0.010 0.001 PHE A 163 TRP 0.006 0.002 TRP A 175 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3161) covalent geometry : angle 0.48934 / 0.26 ( 4304) hydrogen bonds : bond 0.04591 / 2.82 ( 167) hydrogen bonds : angle 4.14991 / 2.92 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.134 Fit side-chains REVERT: A 6 LYS cc_start: 0.8507 (mttt) cc_final: 0.8251 (mttp) REVERT: A 208 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7193 (ttp-170) REVERT: A 214 GLU cc_start: 0.7044 (mp0) cc_final: 0.6506 (tp30) REVERT: A 317 GLU cc_start: 0.7722 (pt0) cc_final: 0.7367 (mt-10) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.6294 time to fit residues: 38.6131 Evaluate side-chains 50 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.0040 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.0040 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.133478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.113579 restraints weight = 3078.783| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.37 r_work: 0.2882 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.104 Angle : 0.457 4.580 4304 Z= 0.245 Chirality : 0.038 0.189 480 Planarity : 0.003 0.031 543 Dihedral : 8.825 60.341 516 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.88 % Allowed : 14.10 % Favored : 83.01 % 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 are not related in a simple way. whole: 2.44 (0.43), residues: 372 helix: 2.04 (0.36), residues: 220 sheet: 2.39 (1.55), residues: 14 loop : 1.01 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.014 0.001 TYR A 361 PHE 0.009 0.001 PHE A 163 TRP 0.005 0.002 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 3161) covalent geometry : angle 0.45736 / 0.24 ( 4304) hydrogen bonds : bond 0.04190 / 2.56 ( 167) hydrogen bonds : angle 4.00097 / 2.82 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.125 Fit side-chains REVERT: A 6 LYS cc_start: 0.8488 (mttt) cc_final: 0.8233 (mttp) REVERT: A 214 GLU cc_start: 0.7024 (mp0) cc_final: 0.6481 (tp30) REVERT: A 317 GLU cc_start: 0.7730 (pt0) cc_final: 0.7396 (mt-10) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.7692 time to fit residues: 42.3159 Evaluate side-chains 59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.131268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.110318 restraints weight = 3058.973| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.04 r_work: 0.2836 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.130 Angle : 0.494 4.792 4304 Z= 0.261 Chirality : 0.039 0.188 480 Planarity : 0.004 0.030 543 Dihedral : 8.902 60.361 516 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.53 % Allowed : 13.78 % Favored : 82.69 % 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 are not related in a simple way. whole: 2.38 (0.43), residues: 372 helix: 2.00 (0.35), residues: 220 sheet: 2.46 (1.55), residues: 14 loop : 0.95 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.016 0.001 TYR A 361 PHE 0.010 0.002 PHE A 270 TRP 0.008 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 3161) covalent geometry : angle 0.49374 / 0.26 ( 4304) hydrogen bonds : bond 0.04737 / 2.88 ( 167) hydrogen bonds : angle 4.05713 / 2.85 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.127 Fit side-chains REVERT: A 6 LYS cc_start: 0.8532 (mttt) cc_final: 0.8293 (mttt) REVERT: A 41 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 214 GLU cc_start: 0.7028 (mp0) cc_final: 0.6480 (tp30) REVERT: A 317 GLU cc_start: 0.7781 (pt0) cc_final: 0.7461 (mt-10) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.6386 time to fit residues: 39.1751 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.117242 restraints weight = 3091.015| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 0.68 r_work: 0.2881 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3161 Z= 0.102 Angle : 0.452 4.663 4304 Z= 0.242 Chirality : 0.038 0.191 480 Planarity : 0.003 0.031 543 Dihedral : 8.758 60.276 516 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.53 % Allowed : 13.46 % Favored : 83.01 % 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 are not related in a simple way. whole: 2.54 (0.44), residues: 372 helix: 2.12 (0.36), residues: 220 sheet: 2.52 (1.57), residues: 14 loop : 1.04 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.013 0.001 TYR A 361 PHE 0.009 0.001 PHE A 163 TRP 0.005 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 3161) covalent geometry : angle 0.45196 / 0.24 ( 4304) hydrogen bonds : bond 0.04126 / 2.53 ( 167) hydrogen bonds : angle 3.93962 / 2.77 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.075 Fit side-chains REVERT: A 6 LYS cc_start: 0.8594 (mttt) cc_final: 0.8368 (mttp) REVERT: A 41 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7690 (t0) REVERT: A 214 GLU cc_start: 0.7171 (mp0) cc_final: 0.6609 (tp30) REVERT: A 317 GLU cc_start: 0.7848 (pt0) cc_final: 0.7580 (mt-10) outliers start: 11 outliers final: 8 residues processed: 58 average time/residue: 0.6872 time to fit residues: 40.6328 Evaluate side-chains 56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.133944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.114008 restraints weight = 3132.866| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.12 r_work: 0.2897 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3161 Z= 0.099 Angle : 0.451 4.629 4304 Z= 0.240 Chirality : 0.038 0.187 480 Planarity : 0.003 0.032 543 Dihedral : 8.684 60.236 516 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.17 % Allowed : 13.14 % Favored : 82.69 % 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 are not related in a simple way. whole: 2.65 (0.44), residues: 372 helix: 2.20 (0.36), residues: 220 sheet: 2.57 (1.58), residues: 14 loop : 1.10 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.013 0.001 TYR A 361 PHE 0.009 0.001 PHE A 270 TRP 0.005 0.001 TRP A 281 HIS 0.001 0.000 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 3161) covalent geometry : angle 0.45057 / 0.24 ( 4304) hydrogen bonds : bond 0.03999 / 2.45 ( 167) hydrogen bonds : angle 3.86967 / 2.72 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.118 Fit side-chains REVERT: A 6 LYS cc_start: 0.8500 (mttt) cc_final: 0.8253 (mttp) REVERT: A 41 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7628 (t0) REVERT: A 214 GLU cc_start: 0.7052 (mp0) cc_final: 0.6539 (tp30) REVERT: A 317 GLU cc_start: 0.7716 (pt0) cc_final: 0.7475 (mt-10) outliers start: 13 outliers final: 7 residues processed: 58 average time/residue: 0.7580 time to fit residues: 44.8140 Evaluate side-chains 54 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 0.0370 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 overall best weight: 2.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.131026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.111580 restraints weight = 3137.282| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.07 r_work: 0.2753 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.136 Angle : 0.510 6.250 4304 Z= 0.267 Chirality : 0.040 0.189 480 Planarity : 0.004 0.030 543 Dihedral : 8.852 60.294 516 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.21 % Allowed : 14.74 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.43), residues: 372 helix: 2.04 (0.35), residues: 220 sheet: 2.64 (1.55), residues: 14 loop : 0.95 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 93 TYR 0.017 0.002 TYR A 360 PHE 0.011 0.002 PHE A 289 TRP 0.008 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3161) covalent geometry : angle 0.50979 / 0.27 ( 4304) hydrogen bonds : bond 0.04803 / 2.91 ( 167) hydrogen bonds : angle 4.02763 / 2.84 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.142 Fit side-chains REVERT: A 6 LYS cc_start: 0.8558 (mttt) cc_final: 0.8301 (mttp) REVERT: A 17 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 41 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7627 (t0) REVERT: A 214 GLU cc_start: 0.7097 (mp0) cc_final: 0.6583 (tp30) REVERT: A 317 GLU cc_start: 0.7776 (pt0) cc_final: 0.7548 (mt-10) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.7093 time to fit residues: 40.5799 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.130902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.113198 restraints weight = 3026.217| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.97 r_work: 0.2811 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3161 Z= 0.128 Angle : 0.499 5.344 4304 Z= 0.263 Chirality : 0.039 0.190 480 Planarity : 0.004 0.030 543 Dihedral : 8.862 60.239 516 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.21 % Allowed : 14.74 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.44), residues: 372 helix: 2.02 (0.35), residues: 220 sheet: 2.61 (1.54), residues: 14 loop : 0.93 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.016 0.001 TYR A 361 PHE 0.011 0.002 PHE A 270 TRP 0.007 0.002 TRP A 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3161) covalent geometry : angle 0.49918 / 0.26 ( 4304) hydrogen bonds : bond 0.04676 / 2.84 ( 167) hydrogen bonds : angle 4.03358 / 2.84 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.077 Fit side-chains REVERT: A 6 LYS cc_start: 0.8509 (mttt) cc_final: 0.8249 (mttp) REVERT: A 41 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7621 (t0) REVERT: A 214 GLU cc_start: 0.7045 (mp0) cc_final: 0.6613 (tp30) REVERT: A 317 GLU cc_start: 0.7711 (pt0) cc_final: 0.7509 (mt-10) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.4819 time to fit residues: 27.0808 Evaluate side-chains 55 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.0501 > 50: distance: 1 - 24: 34.564 distance: 5 - 35: 36.221 distance: 10 - 46: 22.371 distance: 19 - 24: 33.873 distance: 20 - 53: 27.732 distance: 24 - 25: 35.458 distance: 25 - 26: 35.238 distance: 25 - 28: 43.981 distance: 26 - 27: 22.250 distance: 26 - 35: 47.835 distance: 27 - 61: 50.553 distance: 28 - 29: 9.098 distance: 29 - 30: 23.289 distance: 30 - 31: 10.515 distance: 31 - 32: 10.686 distance: 32 - 33: 8.439 distance: 32 - 34: 26.730 distance: 35 - 36: 42.236 distance: 36 - 37: 21.236 distance: 36 - 39: 37.708 distance: 37 - 38: 15.989 distance: 37 - 46: 43.145 distance: 38 - 70: 21.332 distance: 39 - 40: 42.131 distance: 40 - 41: 42.366 distance: 40 - 42: 32.364 distance: 41 - 43: 28.610 distance: 42 - 44: 9.933 distance: 43 - 45: 40.372 distance: 44 - 45: 6.924 distance: 46 - 47: 30.156 distance: 47 - 48: 28.800 distance: 47 - 50: 30.597 distance: 48 - 49: 45.324 distance: 48 - 53: 55.835 distance: 49 - 79: 42.324 distance: 50 - 52: 37.771 distance: 53 - 54: 11.959 distance: 54 - 57: 41.442 distance: 56 - 88: 16.101 distance: 57 - 58: 47.654 distance: 57 - 59: 40.461 distance: 58 - 60: 38.744 distance: 62 - 63: 40.529 distance: 62 - 65: 23.409 distance: 63 - 64: 21.272 distance: 63 - 70: 31.207 distance: 64 - 96: 10.772 distance: 65 - 66: 60.098 distance: 66 - 67: 56.980 distance: 67 - 68: 38.949 distance: 70 - 71: 27.896 distance: 71 - 72: 42.306 distance: 71 - 74: 10.880 distance: 72 - 79: 39.514 distance: 74 - 75: 15.452 distance: 75 - 76: 56.308 distance: 76 - 77: 41.204 distance: 76 - 78: 31.671 distance: 79 - 80: 17.904 distance: 80 - 81: 40.660 distance: 80 - 83: 13.314 distance: 81 - 82: 17.341 distance: 81 - 88: 32.324 distance: 83 - 84: 6.679 distance: 84 - 85: 51.421 distance: 85 - 86: 49.005 distance: 85 - 87: 7.980 distance: 88 - 89: 24.419 distance: 89 - 90: 12.122 distance: 89 - 92: 10.640 distance: 90 - 96: 57.627 distance: 92 - 93: 31.489 distance: 93 - 94: 11.110 distance: 93 - 95: 33.509 distance: 96 - 97: 24.655 distance: 97 - 98: 40.613 distance: 97 - 100: 31.443 distance: 98 - 99: 10.617 distance: 98 - 105: 35.711 distance: 100 - 101: 21.342 distance: 101 - 102: 38.732 distance: 102 - 104: 45.760 distance: 105 - 106: 30.907 distance: 106 - 107: 34.913 distance: 106 - 109: 45.701 distance: 107 - 108: 17.936 distance: 107 - 113: 27.294 distance: 110 - 112: 37.082