Starting phenix.real_space_refine on Wed Jul 1 22:26:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lcj_23275/07_2026/7lcj_23275.cif" } resolution = 2.82 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= 0.091 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 S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 571 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 3264 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 58 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 17} Link IDs: {None: 17} Time building chain proxies: 0.75, per 1000 atoms: 0.23 Number of scatterers: 3264 At special positions: 0 Unit cell: (60.079, 116.866, 69.955, 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 18 16.00 F 1 9.00 O 571 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 72.2 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 70.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.918A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.604A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 Processing helix chain 'R' and resid 202 through 207 removed outlier: 3.510A pdb=" N SER R 206 " --> pdb=" O LYS R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 3.944A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.705A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.800A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.848A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing helix chain 'R' and resid 377 through 392 Processing helix chain 'R' and resid 393 through 404 Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.547A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 597 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: 0.40 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 974 1.41 - 1.54: 1861 1.54 - 1.68: 6 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.44e-02 4.82e+03 1.17e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 4503 3.63 - 7.26: 63 7.26 - 10.88: 3 10.88 - 14.51: 1 14.51 - 18.14: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" C SER R 136 " pdb=" N PRO R 137 " pdb=" CA PRO R 137 " ideal model delta sigma weight residual 119.28 126.40 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta sigma weight residual 110.67 122.36 -11.69 1.92e+00 2.71e-01 3.71e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.12 18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C LEU R 89 " pdb=" N PRO R 90 " pdb=" CA PRO R 90 " ideal model delta sigma weight residual 119.28 125.52 -6.24 1.10e+00 8.26e-01 3.21e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.79 119.63 -8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1733 17.85 - 35.70: 154 35.70 - 53.55: 26 53.55 - 71.39: 3 71.39 - 89.24: 2 Dihedral angle restraints: 1918 sinusoidal: 762 harmonic: 1156 Sorted by residual: dihedral pdb=" C THR R 362 " pdb=" N THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta harmonic sigma weight residual -122.00 -143.04 21.04 0 2.50e+00 1.60e-01 7.08e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -142.72 56.72 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 ... (remaining 1915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 466 0.145 - 0.290: 27 0.290 - 0.435: 2 0.435 - 0.580: 1 0.580 - 0.724: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR R 362 " pdb=" N THR R 362 " pdb=" C THR R 362 " pdb=" CB THR R 362 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA TRP R 243 " pdb=" N TRP R 243 " pdb=" C TRP R 243 " pdb=" CB TRP R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 355 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR R 355 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 355 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 356 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ILE R 146 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 277 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " 0.027 5.00e-02 4.00e+02 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 3196 3.29 - 3.83: 5221 3.83 - 4.36: 6319 4.36 - 4.90: 10614 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.216 3.120 nonbonded pdb=" O GLY R 98 " pdb=" ND1 HIS R 99 " model vdw 2.335 3.120 nonbonded pdb=" O GLU R 408 " pdb=" OE1 GLU R 412 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU R 76 " pdb=" OG SER R 79 " model vdw 2.342 3.040 nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.383 3.120 ... (remaining 25782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 3.600 Find NCS groups from input model: 0.010 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.011 0.114 3355 Z= 0.600 Angle : 1.187 18.141 4579 Z= 0.785 Chirality : 0.083 0.724 497 Planarity : 0.006 0.049 557 Dihedral : 13.355 89.243 1158 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.67 % Cbeta Deviations : 0.80 % 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: 0.54 (0.41), residues: 386 helix: 1.08 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 299 TYR 0.023 0.003 TYR R 148 PHE 0.017 0.003 PHE R 280 TRP 0.019 0.002 TRP R 243 HIS 0.006 0.002 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.01051 / 0.60 ( 3351) covalent geometry : angle 1.18750 / 0.79 ( 4571) SS BOND : bond 0.00473 / 0.23 ( 4) SS BOND : angle 1.07309 / 0.65 ( 8) hydrogen bonds : bond 0.19748 / 13.03 ( 199) hydrogen bonds : angle 6.40481 / 4.49 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.073 Fit side-chains REVERT: R 41 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6643 (mm-30) REVERT: R 416 SER cc_start: 0.6812 (t) cc_final: 0.6581 (m) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.3644 time to fit residues: 13.6756 Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 45 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.204924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134779 restraints weight = 3307.549| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.12 r_work: 0.3368 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.139 Angle : 0.568 7.222 4579 Z= 0.305 Chirality : 0.037 0.130 497 Planarity : 0.004 0.050 557 Dihedral : 4.745 28.638 444 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.16 % Allowed : 8.14 % Favored : 90.70 % 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: 1.66 (0.43), residues: 386 helix: 2.03 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.81 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.028 0.002 TYR R 148 PHE 0.016 0.001 PHE R 143 TRP 0.015 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 3351) covalent geometry : angle 0.56757 / 0.30 ( 4571) SS BOND : bond 0.00156 / 0.07 ( 4) SS BOND : angle 0.82982 / 0.49 ( 8) hydrogen bonds : bond 0.06847 / 4.42 ( 199) hydrogen bonds : angle 3.95354 / 2.89 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.093 Fit side-chains REVERT: R 41 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7017 (mp0) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.2984 time to fit residues: 9.3934 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 212 HIS ** 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 = 0.4236 r_free = 0.4236 target = 0.204847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134889 restraints weight = 3289.098| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.08 r_work: 0.3365 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3355 Z= 0.123 Angle : 0.508 7.178 4579 Z= 0.268 Chirality : 0.036 0.132 497 Planarity : 0.004 0.057 557 Dihedral : 4.338 29.900 442 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.43), residues: 386 helix: 2.40 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.69 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 326 TYR 0.027 0.001 TYR R 148 PHE 0.011 0.001 PHE R 143 TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 3351) covalent geometry : angle 0.50732 / 0.27 ( 4571) SS BOND : bond 0.00161 / 0.08 ( 4) SS BOND : angle 0.68905 / 0.38 ( 8) hydrogen bonds : bond 0.06129 / 3.96 ( 199) hydrogen bonds : angle 3.72052 / 2.73 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.122 Fit side-chains REVERT: R 41 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6870 (mm-30) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.4212 time to fit residues: 11.9190 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.202518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131967 restraints weight = 3284.073| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.10 r_work: 0.3325 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3355 Z= 0.139 Angle : 0.530 9.671 4579 Z= 0.276 Chirality : 0.037 0.128 497 Planarity : 0.004 0.059 557 Dihedral : 4.389 31.006 442 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.03 % Allowed : 12.21 % Favored : 85.76 % 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: 2.09 (0.43), residues: 386 helix: 2.35 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.61 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 414 TYR 0.027 0.002 TYR R 148 PHE 0.011 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 3351) covalent geometry : angle 0.53037 / 0.28 ( 4571) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 0.58095 / 0.30 ( 8) hydrogen bonds : bond 0.06611 / 4.28 ( 199) hydrogen bonds : angle 3.73723 / 2.71 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.124 Fit side-chains REVERT: R 41 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6819 (mm-30) REVERT: R 384 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7862 (mm) REVERT: R 414 ARG cc_start: 0.6289 (mmt90) cc_final: 0.5258 (mmp-170) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.3975 time to fit residues: 12.5084 Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.203155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132757 restraints weight = 3295.623| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.11 r_work: 0.3334 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.130 Angle : 0.513 9.411 4579 Z= 0.267 Chirality : 0.037 0.127 497 Planarity : 0.004 0.059 557 Dihedral : 4.311 30.543 442 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 12.21 % Favored : 85.17 % 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: 2.20 (0.43), residues: 386 helix: 2.43 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.62 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.025 0.001 TYR R 148 PHE 0.011 0.001 PHE R 280 TRP 0.019 0.001 TRP R 243 HIS 0.003 0.001 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 3351) covalent geometry : angle 0.51256 / 0.27 ( 4571) SS BOND : bond 0.00172 / 0.08 ( 4) SS BOND : angle 0.57393 / 0.29 ( 8) hydrogen bonds : bond 0.06261 / 4.04 ( 199) hydrogen bonds : angle 3.66175 / 2.64 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.146 Fit side-chains REVERT: R 41 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6846 (mm-30) REVERT: R 159 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7710 (mt) REVERT: R 384 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7874 (mm) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 0.3798 time to fit residues: 12.7825 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.202050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131043 restraints weight = 3283.006| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3355 Z= 0.141 Angle : 0.525 9.749 4579 Z= 0.272 Chirality : 0.037 0.128 497 Planarity : 0.004 0.059 557 Dihedral : 4.371 30.758 442 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 13.37 % Favored : 84.30 % 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: 2.16 (0.43), residues: 386 helix: 2.37 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 414 TYR 0.026 0.002 TYR R 148 PHE 0.011 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.003 0.001 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 3351) covalent geometry : angle 0.52545 / 0.27 ( 4571) SS BOND : bond 0.00189 / 0.09 ( 4) SS BOND : angle 0.52789 / 0.27 ( 8) hydrogen bonds : bond 0.06625 / 4.28 ( 199) hydrogen bonds : angle 3.71483 / 2.67 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.115 Fit side-chains REVERT: R 41 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6961 (mm-30) REVERT: R 159 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (mt) REVERT: R 384 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7922 (mm) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.4003 time to fit residues: 13.4052 Evaluate side-chains 34 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.201588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130570 restraints weight = 3300.966| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3355 Z= 0.144 Angle : 0.528 9.895 4579 Z= 0.273 Chirality : 0.037 0.128 497 Planarity : 0.004 0.058 557 Dihedral : 4.370 30.485 442 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 14.24 % Favored : 83.14 % 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: 2.16 (0.42), residues: 386 helix: 2.38 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.026 0.002 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3351) covalent geometry : angle 0.52768 / 0.27 ( 4571) SS BOND : bond 0.00190 / 0.09 ( 4) SS BOND : angle 0.53443 / 0.27 ( 8) hydrogen bonds : bond 0.06742 / 4.35 ( 199) hydrogen bonds : angle 3.73038 / 2.67 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.118 Fit side-chains REVERT: R 41 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6941 (mm-30) REVERT: R 159 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7766 (mt) REVERT: R 384 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7898 (mm) outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 0.3621 time to fit residues: 12.5878 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 58.1747 > 50: distance: 12 - 102: 34.667 distance: 54 - 63: 28.041 distance: 63 - 64: 21.741 distance: 64 - 65: 47.688 distance: 64 - 67: 8.139 distance: 65 - 66: 26.010 distance: 65 - 71: 35.148 distance: 67 - 68: 23.177 distance: 68 - 69: 18.956 distance: 68 - 70: 25.411 distance: 71 - 72: 27.009 distance: 72 - 73: 16.038 distance: 72 - 75: 42.043 distance: 73 - 74: 18.455 distance: 73 - 80: 16.144 distance: 75 - 76: 16.726 distance: 76 - 77: 24.300 distance: 77 - 78: 12.068 distance: 77 - 79: 3.968 distance: 80 - 81: 23.759 distance: 81 - 82: 14.253 distance: 81 - 84: 11.532 distance: 82 - 83: 20.122 distance: 82 - 92: 20.037 distance: 84 - 85: 14.456 distance: 85 - 86: 4.847 distance: 85 - 87: 10.439 distance: 86 - 88: 9.401 distance: 87 - 89: 11.738 distance: 88 - 90: 8.340 distance: 89 - 90: 5.365 distance: 90 - 91: 17.696 distance: 92 - 93: 28.094 distance: 93 - 94: 21.255 distance: 93 - 96: 21.325 distance: 94 - 95: 13.175 distance: 94 - 97: 12.025 distance: 97 - 98: 12.194 distance: 98 - 99: 8.415 distance: 98 - 101: 9.505 distance: 99 - 100: 21.133 distance: 99 - 103: 29.152 distance: 101 - 102: 32.373 distance: 103 - 104: 31.565 distance: 104 - 105: 22.902 distance: 104 - 107: 17.240 distance: 105 - 106: 4.559 distance: 105 - 117: 13.089 distance: 107 - 108: 12.705 distance: 108 - 109: 20.900 distance: 108 - 110: 4.703 distance: 109 - 111: 7.221 distance: 110 - 112: 5.650 distance: 110 - 113: 12.546 distance: 111 - 112: 9.094 distance: 112 - 114: 7.991 distance: 113 - 115: 8.658 distance: 114 - 116: 12.300 distance: 115 - 116: 8.788 distance: 117 - 118: 25.163 distance: 117 - 123: 31.534 distance: 118 - 119: 10.474 distance: 118 - 121: 14.881 distance: 119 - 120: 17.519 distance: 119 - 124: 11.520 distance: 121 - 122: 19.901 distance: 122 - 123: 36.456 distance: 124 - 125: 3.736 distance: 125 - 126: 3.746 distance: 125 - 128: 13.762 distance: 126 - 127: 13.525 distance: 126 - 132: 7.491 distance: 128 - 129: 16.936 distance: 129 - 130: 19.181 distance: 129 - 131: 4.680 distance: 132 - 133: 17.929 distance: 133 - 134: 7.917 distance: 134 - 135: 25.249 distance: 134 - 136: 12.327 distance: 136 - 137: 12.024 distance: 137 - 138: 11.065 distance: 137 - 140: 11.885 distance: 138 - 139: 9.941 distance: 138 - 145: 10.584 distance: 140 - 141: 16.190 distance: 141 - 142: 20.911 distance: 142 - 143: 15.667 distance: 142 - 144: 7.011