Starting phenix.real_space_refine on Thu Jul 2 06:42:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iu0_35713/07_2026/8iu0_35713.cif" } resolution = 2.66 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= 0.004 sd= 0.125 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 9 5.49 5 S 60 5.16 5 C 4863 2.51 5 N 954 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s 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: 7062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4, 'PSC:plan-1': 6, 'PSC:plan-2': 6} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 35 " occ=0.50 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 35 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 35 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7062 At special positions: 0 Unit cell: (77.19, 77.19, 84.66, 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 60 16.00 P 9 15.00 O 1176 8.00 N 954 7.00 C 4863 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 474.3 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.781A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.122A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 426 hydrogen bonds defined for protein. 1281 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: 0.94 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1226 1.33 - 1.46: 2621 1.46 - 1.59: 3260 1.59 - 1.72: 15 1.72 - 1.85: 81 Bond restraints: 7203 Sorted by residual: bond pdb=" C7 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC A 311 " pdb=" C4 PSC A 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC B 311 " pdb=" C4 PSC B 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC C 311 " pdb=" C4 PSC C 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 1.530 1.320 0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 9164 3.02 - 6.03: 409 6.03 - 9.05: 18 9.05 - 12.07: 21 12.07 - 15.08: 18 Bond angle restraints: 9630 Sorted by residual: angle pdb=" C10 PSC B 310 " pdb=" C9 PSC B 310 " pdb=" C8 PSC B 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC A 310 " pdb=" C9 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC C 310 " pdb=" C9 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 127.68 112.61 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC B 310 " pdb=" C11 PSC B 310 " pdb=" C12 PSC B 310 " ideal model delta sigma weight residual 111.07 126.14 -15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC A 310 " pdb=" C11 PSC A 310 " pdb=" C12 PSC A 310 " ideal model delta sigma weight residual 111.07 126.12 -15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 9625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3690 23.98 - 47.95: 294 47.95 - 71.93: 90 71.93 - 95.90: 0 95.90 - 119.88: 3 Dihedral angle restraints: 4077 sinusoidal: 1824 harmonic: 2253 Sorted by residual: dihedral pdb=" C03 PSC C 302 " pdb=" O11 PSC C 302 " pdb=" P PSC C 302 " pdb=" O12 PSC C 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.58 119.88 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC A 302 " pdb=" O11 PSC A 302 " pdb=" P PSC A 302 " pdb=" O12 PSC A 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.59 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC B 302 " pdb=" O11 PSC B 302 " pdb=" P PSC B 302 " pdb=" O12 PSC B 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.60 119.86 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 457 0.051 - 0.102: 326 0.102 - 0.153: 113 0.153 - 0.204: 31 0.204 - 0.255: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 147 " pdb=" N PRO C 147 " pdb=" C PRO C 147 " pdb=" CB PRO C 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 933 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C11 PSC B 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC B 312 " -0.100 2.00e-02 2.50e+03 pdb=" C9 PSC B 312 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC A 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC A 312 " -0.099 2.00e-02 2.50e+03 pdb=" C9 PSC A 312 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 312 " 0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC C 312 " -0.102 2.00e-02 2.50e+03 pdb=" C8 PSC C 312 " 0.099 2.00e-02 2.50e+03 pdb=" C9 PSC C 312 " -0.307 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1588 2.79 - 3.32: 6677 3.32 - 3.84: 12411 3.84 - 4.37: 15914 4.37 - 4.90: 25235 Nonbonded interactions: 61825 Sorted by model distance: nonbonded pdb=" OH TYR A 103 " pdb=" O HOH A 401 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 103 " pdb=" O HOH C 401 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 103 " pdb=" O HOH B 401 " model vdw 2.259 3.040 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 309 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG A 171 " pdb=" O13 PSC A 309 " model vdw 2.306 3.120 ... (remaining 61820 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=0.99 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: 0.410 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.820 Find NCS groups from input model: 0.040 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.015 0.211 7206 Z= 0.877 Angle : 1.596 15.084 9630 Z= 0.937 Chirality : 0.077 0.255 936 Planarity : 0.023 0.230 1158 Dihedral : 17.842 119.879 2649 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 4.95 % Favored : 94.14 % 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: -1.94 (0.27), residues: 780 helix: -1.30 (0.19), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG A 151 TYR 0.044 0.009 TYR A 150 PHE 0.035 0.008 PHE B 243 TRP 0.038 0.011 TRP B 187 HIS 0.011 0.006 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.01442 / 0.81 ( 7203) covalent geometry : angle 1.59597 / 0.94 ( 9630) hydrogen bonds : bond 0.19736 / 13.26 ( 426) hydrogen bonds : angle 7.30892 / 5.46 ( 1281) Misc. bond : bond 0.16773 / 8.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.198 Fit side-chains REVERT: A 207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm) REVERT: A 230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp) REVERT: B 207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm) REVERT: C 207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 0.5955 time to fit residues: 49.3071 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108178 restraints weight = 22141.613| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.08 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7206 Z= 0.236 Angle : 1.002 11.530 9630 Z= 0.520 Chirality : 0.058 0.479 936 Planarity : 0.011 0.112 1158 Dihedral : 18.264 104.993 1268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.14 % Favored : 94.33 % Rotamer: Outliers : 1.80 % Allowed : 8.11 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.28), residues: 780 helix: -0.73 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG B 128 TYR 0.106 0.005 TYR B 155 PHE 0.105 0.006 PHE C 134 TRP 0.113 0.010 TRP B 138 HIS 0.017 0.004 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.24 ( 7203) covalent geometry : angle 1.00185 / 0.52 ( 9630) hydrogen bonds : bond 0.07106 / 4.75 ( 426) hydrogen bonds : angle 5.09937 / 3.81 ( 1281) Misc. bond : bond 0.00034 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.245 Fit side-chains REVERT: A 87 ASP cc_start: 0.8685 (t70) cc_final: 0.8420 (t70) REVERT: A 248 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7846 (mt-10) REVERT: B 171 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7509 (ttm110) REVERT: C 174 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8067 (mttm) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.5404 time to fit residues: 47.3306 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103573 restraints weight = 37057.496| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.54 r_work: 0.3083 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7206 Z= 0.123 Angle : 0.536 5.889 9630 Z= 0.265 Chirality : 0.040 0.126 936 Planarity : 0.005 0.060 1158 Dihedral : 14.824 82.546 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.10 % Allowed : 8.11 % Favored : 89.79 % 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: 1.22 (0.30), residues: 780 helix: 1.25 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.10 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.012 0.001 TYR C 81 PHE 0.018 0.001 PHE C 221 TRP 0.019 0.002 TRP B 42 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7203) covalent geometry : angle 0.53561 / 0.26 ( 9630) hydrogen bonds : bond 0.04790 / 3.14 ( 426) hydrogen bonds : angle 3.96473 / 2.96 ( 1281) Misc. bond : bond 0.00054 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.271 Fit side-chains REVERT: A 87 ASP cc_start: 0.8648 (t70) cc_final: 0.8357 (t70) REVERT: B 80 MET cc_start: 0.8752 (mtp) cc_final: 0.8515 (mtt) REVERT: C 121 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 225 PHE cc_start: 0.8603 (m-80) cc_final: 0.8254 (m-10) REVERT: C 244 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8238 (mtp180) outliers start: 11 outliers final: 0 residues processed: 81 average time/residue: 0.5400 time to fit residues: 46.0814 Evaluate side-chains 67 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102098 restraints weight = 30647.268| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.33 r_work: 0.3073 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7206 Z= 0.134 Angle : 0.544 5.924 9630 Z= 0.261 Chirality : 0.040 0.124 936 Planarity : 0.004 0.049 1158 Dihedral : 13.023 60.299 1266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.05 % Allowed : 9.01 % Favored : 89.94 % 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: 2.24 (0.30), residues: 780 helix: 2.06 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.16 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 176 TYR 0.010 0.001 TYR C 81 PHE 0.016 0.001 PHE A 134 TRP 0.016 0.002 TRP B 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7203) covalent geometry : angle 0.54376 / 0.26 ( 9630) hydrogen bonds : bond 0.05159 / 3.39 ( 426) hydrogen bonds : angle 3.85612 / 2.87 ( 1281) Misc. bond : bond 0.00071 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.251 Fit side-chains REVERT: A 87 ASP cc_start: 0.8694 (t70) cc_final: 0.8377 (t70) REVERT: B 80 MET cc_start: 0.8854 (mtp) cc_final: 0.8531 (mtt) REVERT: B 174 LYS cc_start: 0.8149 (mttm) cc_final: 0.7908 (mttp) REVERT: C 80 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: C 244 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8278 (mtp180) outliers start: 4 outliers final: 1 residues processed: 74 average time/residue: 0.4832 time to fit residues: 37.9167 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain C residue 80 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.126577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103199 restraints weight = 39197.893| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.60 r_work: 0.3069 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7206 Z= 0.120 Angle : 0.513 6.167 9630 Z= 0.245 Chirality : 0.039 0.121 936 Planarity : 0.004 0.042 1158 Dihedral : 11.939 57.314 1266 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.65 % Allowed : 8.71 % Favored : 89.64 % 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: 2.62 (0.29), residues: 780 helix: 2.36 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.25 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.009 0.001 TYR C 81 PHE 0.018 0.001 PHE C 221 TRP 0.015 0.001 TRP A 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7203) covalent geometry : angle 0.51282 / 0.24 ( 9630) hydrogen bonds : bond 0.04692 / 3.08 ( 426) hydrogen bonds : angle 3.75396 / 2.79 ( 1281) Misc. bond : bond 0.00052 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.250 Fit side-chains REVERT: A 87 ASP cc_start: 0.8700 (t70) cc_final: 0.8386 (t70) REVERT: A 121 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 254 GLN cc_start: 0.8275 (mt0) cc_final: 0.7969 (mt0) REVERT: B 80 MET cc_start: 0.8837 (mtp) cc_final: 0.8528 (mtt) REVERT: C 80 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: C 121 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8043 (mt) REVERT: C 244 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8203 (mtm-85) outliers start: 8 outliers final: 0 residues processed: 69 average time/residue: 0.4578 time to fit residues: 33.7281 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 5 optimal weight: 0.0870 overall best weight: 2.0100 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101395 restraints weight = 36618.579| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.50 r_work: 0.3041 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7206 Z= 0.139 Angle : 0.548 6.708 9630 Z= 0.259 Chirality : 0.041 0.125 936 Planarity : 0.004 0.038 1158 Dihedral : 12.242 59.130 1266 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.65 % Allowed : 8.26 % Favored : 90.09 % 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: 2.63 (0.29), residues: 780 helix: 2.36 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.29 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.011 0.001 TYR C 81 PHE 0.016 0.001 PHE A 134 TRP 0.013 0.002 TRP A 42 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7203) covalent geometry : angle 0.54769 / 0.26 ( 9630) hydrogen bonds : bond 0.05268 / 3.47 ( 426) hydrogen bonds : angle 3.81121 / 2.84 ( 1281) Misc. bond : bond 0.00059 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.153 Fit side-chains REVERT: A 87 ASP cc_start: 0.8729 (t70) cc_final: 0.8430 (t70) REVERT: B 80 MET cc_start: 0.8878 (mtp) cc_final: 0.8534 (mtp) REVERT: C 80 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8451 (mtp) REVERT: C 121 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 244 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8239 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.4916 time to fit residues: 34.4503 Evaluate side-chains 63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 0.0970 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.132022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108971 restraints weight = 33829.439| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.46 r_work: 0.3154 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7206 Z= 0.096 Angle : 0.468 6.655 9630 Z= 0.221 Chirality : 0.037 0.122 936 Planarity : 0.004 0.034 1158 Dihedral : 10.373 59.870 1266 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.50 % Allowed : 8.71 % Favored : 89.79 % 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: 3.06 (0.30), residues: 780 helix: 2.73 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.31 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.008 0.001 TYR C 81 PHE 0.013 0.001 PHE A 134 TRP 0.015 0.001 TRP A 42 HIS 0.003 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 7203) covalent geometry : angle 0.46775 / 0.22 ( 9630) hydrogen bonds : bond 0.03712 / 2.40 ( 426) hydrogen bonds : angle 3.56047 / 2.64 ( 1281) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.246 Fit side-chains REVERT: A 87 ASP cc_start: 0.8608 (t70) cc_final: 0.8339 (t70) REVERT: A 225 PHE cc_start: 0.8136 (m-10) cc_final: 0.7789 (m-80) REVERT: B 80 MET cc_start: 0.8745 (mtp) cc_final: 0.8505 (mtt) REVERT: C 80 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8491 (mtt) REVERT: C 244 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8236 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.5212 time to fit residues: 40.2809 Evaluate side-chains 59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 80 MET 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: 68.1291 > 50: distance: 17 - 35: 29.412 distance: 21 - 43: 31.983 distance: 26 - 51: 23.790 distance: 29 - 35: 31.976 distance: 30 - 62: 25.835 distance: 35 - 36: 22.943 distance: 36 - 37: 11.216 distance: 36 - 39: 36.024 distance: 37 - 38: 46.289 distance: 37 - 43: 3.884 distance: 38 - 67: 33.234 distance: 39 - 40: 19.002 distance: 40 - 41: 38.146 distance: 40 - 42: 14.400 distance: 44 - 45: 32.903 distance: 44 - 47: 51.564 distance: 45 - 46: 19.845 distance: 45 - 51: 35.264 distance: 46 - 78: 48.567 distance: 47 - 48: 29.213 distance: 48 - 49: 9.680 distance: 48 - 50: 31.169 distance: 51 - 52: 10.390 distance: 52 - 53: 23.758 distance: 52 - 55: 18.872 distance: 53 - 54: 4.679 distance: 53 - 62: 32.527 distance: 54 - 85: 33.340 distance: 55 - 56: 20.519 distance: 56 - 57: 16.398 distance: 56 - 58: 23.631 distance: 57 - 59: 16.453 distance: 58 - 60: 20.472 distance: 59 - 61: 11.236 distance: 60 - 61: 9.979 distance: 62 - 63: 9.614 distance: 63 - 64: 5.859 distance: 63 - 66: 19.510 distance: 64 - 65: 7.765 distance: 64 - 67: 19.595 distance: 65 - 93: 42.800 distance: 67 - 68: 5.160 distance: 68 - 69: 13.774 distance: 68 - 71: 20.049 distance: 69 - 70: 36.549 distance: 69 - 78: 12.446 distance: 71 - 72: 23.126 distance: 72 - 73: 12.346 distance: 72 - 74: 36.139 distance: 73 - 75: 23.822 distance: 74 - 76: 10.866 distance: 75 - 77: 18.801 distance: 76 - 77: 23.832 distance: 78 - 79: 31.013 distance: 79 - 80: 26.003 distance: 79 - 82: 11.810 distance: 80 - 81: 39.322 distance: 80 - 85: 28.939 distance: 82 - 83: 34.907 distance: 82 - 84: 50.101 distance: 85 - 86: 14.415 distance: 86 - 87: 17.618 distance: 86 - 89: 55.715 distance: 87 - 88: 31.891 distance: 87 - 93: 13.475 distance: 89 - 90: 34.078 distance: 90 - 91: 12.851 distance: 90 - 92: 37.887 distance: 93 - 94: 3.658 distance: 94 - 95: 40.089 distance: 94 - 97: 36.745 distance: 95 - 96: 10.049 distance: 95 - 101: 52.441 distance: 97 - 98: 16.805 distance: 98 - 99: 14.579 distance: 98 - 100: 9.542 distance: 101 - 102: 5.428 distance: 102 - 103: 24.928 distance: 102 - 105: 18.874 distance: 103 - 104: 40.567 distance: 103 - 109: 9.242 distance: 105 - 106: 27.756 distance: 106 - 107: 21.155 distance: 106 - 108: 41.849 distance: 109 - 110: 19.261 distance: 109 - 115: 16.475 distance: 110 - 111: 11.698 distance: 110 - 113: 17.418 distance: 111 - 112: 17.479 distance: 111 - 116: 9.027 distance: 113 - 114: 17.399 distance: 114 - 115: 17.578