Starting phenix.real_space_refine on Tue Mar 11 23:08:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469.map" model { file = "/net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cde_45469/03_2025/9cde_45469_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 12 5.49 5 S 57 5.16 5 C 4761 2.51 5 N 903 2.21 5 O 1089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1954 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 320 Unusual residues: {'CLR': 3, 'PEE': 4, 'RET': 1} Classifications: {'undetermined': 8, 'water': 12} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Restraints were copied for chains: C, B Time building chain proxies: 4.50, per 1000 atoms: 0.66 Number of scatterers: 6822 At special positions: 0 Unit cell: (80.34, 76.22, 75.19, 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 57 16.00 P 12 15.00 O 1089 8.00 N 903 7.00 C 4761 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 936.1 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.681A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) 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 removed outlier: 3.527A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.568A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 150 through 167 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.827A pdb=" N HIS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.204A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.681A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) 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 removed outlier: 3.527A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.568A pdb=" N ILE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Processing helix chain 'B' and resid 150 through 167 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.826A pdb=" N HIS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.203A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 3.681A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) 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 removed outlier: 3.527A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix removed outlier: 3.568A pdb=" N ILE C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 142 Processing helix chain 'C' and resid 150 through 167 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.827A pdb=" N HIS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.203A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 378 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1399 1.33 - 1.45: 1666 1.45 - 1.57: 3820 1.57 - 1.69: 51 1.69 - 1.81: 90 Bond restraints: 7026 Sorted by residual: bond pdb=" O4P PEE C 305 " pdb=" P PEE C 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4P PEE A 305 " pdb=" P PEE A 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4P PEE B 305 " pdb=" P PEE B 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4P PEE A 306 " pdb=" P PEE A 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O4P PEE B 306 " pdb=" P PEE B 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 7021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9110 2.78 - 5.56: 250 5.56 - 8.34: 90 8.34 - 11.11: 3 11.11 - 13.89: 12 Bond angle restraints: 9465 Sorted by residual: angle pdb=" O1P PEE A 308 " pdb=" P PEE A 308 " pdb=" O2P PEE A 308 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE B 308 " pdb=" P PEE B 308 " pdb=" O2P PEE B 308 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE C 308 " pdb=" P PEE C 308 " pdb=" O2P PEE C 308 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE C 307 " pdb=" P PEE C 307 " pdb=" O2P PEE C 307 " ideal model delta sigma weight residual 119.43 133.27 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE A 306 " pdb=" P PEE A 306 " pdb=" O2P PEE A 306 " ideal model delta sigma weight residual 119.43 133.27 -13.84 3.00e+00 1.11e-01 2.13e+01 ... (remaining 9460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 4236 34.41 - 68.82: 234 68.82 - 103.23: 27 103.23 - 137.64: 12 137.64 - 172.05: 36 Dihedral angle restraints: 4545 sinusoidal: 2451 harmonic: 2094 Sorted by residual: dihedral pdb=" N PEE B 305 " pdb=" C4 PEE B 305 " pdb=" C5 PEE B 305 " pdb=" O4P PEE B 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.08 -172.05 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE A 305 " pdb=" C4 PEE A 305 " pdb=" C5 PEE A 305 " pdb=" O4P PEE A 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.04 -172.01 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE C 305 " pdb=" C4 PEE C 305 " pdb=" C5 PEE C 305 " pdb=" O4P PEE C 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.03 -172.00 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 856 0.087 - 0.173: 53 0.173 - 0.260: 3 0.260 - 0.347: 30 0.347 - 0.433: 15 Chirality restraints: 957 Sorted by residual: chirality pdb=" C2 PEE A 305 " pdb=" C1 PEE A 305 " pdb=" C3 PEE A 305 " pdb=" O2 PEE A 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C2 PEE C 305 " pdb=" C1 PEE C 305 " pdb=" C3 PEE C 305 " pdb=" O2 PEE C 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C2 PEE B 305 " pdb=" C1 PEE B 305 " pdb=" C3 PEE B 305 " pdb=" O2 PEE B 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.67e+00 ... (remaining 954 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET C 301 " -0.027 2.00e-02 2.50e+03 7.21e-02 6.51e+01 pdb=" C13 RET C 301 " 0.049 2.00e-02 2.50e+03 pdb=" C14 RET C 301 " -0.128 2.00e-02 2.50e+03 pdb=" C15 RET C 301 " 0.074 2.00e-02 2.50e+03 pdb=" C20 RET C 301 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET A 301 " 0.027 2.00e-02 2.50e+03 7.19e-02 6.47e+01 pdb=" C13 RET A 301 " -0.049 2.00e-02 2.50e+03 pdb=" C14 RET A 301 " 0.128 2.00e-02 2.50e+03 pdb=" C15 RET A 301 " -0.074 2.00e-02 2.50e+03 pdb=" C20 RET A 301 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 301 " 0.027 2.00e-02 2.50e+03 7.18e-02 6.45e+01 pdb=" C13 RET B 301 " -0.049 2.00e-02 2.50e+03 pdb=" C14 RET B 301 " 0.127 2.00e-02 2.50e+03 pdb=" C15 RET B 301 " -0.074 2.00e-02 2.50e+03 pdb=" C20 RET B 301 " -0.032 2.00e-02 2.50e+03 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 5844 3.18 - 3.75: 10839 3.75 - 4.33: 16239 4.33 - 4.90: 25811 Nonbonded interactions: 58859 Sorted by model distance: nonbonded pdb=" N ILE A 127 " pdb=" OE2 GLU C 65 " model vdw 2.031 3.120 nonbonded pdb=" OE2 GLU B 65 " pdb=" N ILE C 127 " model vdw 2.034 3.120 nonbonded pdb=" OE2 GLU A 65 " pdb=" N ILE B 127 " model vdw 2.036 3.120 nonbonded pdb=" O SER C 168 " pdb=" ND1 HIS C 172 " model vdw 2.254 3.120 nonbonded pdb=" O SER A 168 " pdb=" ND1 HIS A 172 " model vdw 2.254 3.120 ... (remaining 58854 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.009 0.123 7026 Z= 0.583 Angle : 1.152 13.892 9465 Z= 0.425 Chirality : 0.084 0.433 957 Planarity : 0.006 0.072 1044 Dihedral : 25.586 172.045 3213 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.46 % Allowed : 4.88 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.33), residues: 714 helix: 1.71 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 42 HIS 0.001 0.000 HIS C 125 PHE 0.020 0.001 PHE B 196 TYR 0.014 0.002 TYR A 53 ARG 0.002 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 290 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.8437 (p) cc_final: 0.8231 (p) REVERT: A 155 TYR cc_start: 0.8144 (t80) cc_final: 0.7361 (t80) REVERT: A 180 TYR cc_start: 0.6083 (m-10) cc_final: 0.5862 (m-10) REVERT: A 195 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6503 (t80) REVERT: B 65 GLU cc_start: 0.8203 (tp30) cc_final: 0.7670 (mp0) REVERT: B 151 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7587 (ttm170) REVERT: B 155 TYR cc_start: 0.8185 (t80) cc_final: 0.7905 (t80) REVERT: B 185 GLN cc_start: 0.8513 (mt0) cc_final: 0.8303 (mt0) REVERT: B 195 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6230 (t80) REVERT: C 65 GLU cc_start: 0.8175 (tp30) cc_final: 0.7929 (mp0) REVERT: C 101 TYR cc_start: 0.7606 (m-10) cc_final: 0.7135 (m-10) REVERT: C 151 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7738 (ttm170) REVERT: C 155 TYR cc_start: 0.8040 (t80) cc_final: 0.7620 (t80) REVERT: C 177 TYR cc_start: 0.8577 (t80) cc_final: 0.7402 (t80) REVERT: C 180 TYR cc_start: 0.6126 (m-10) cc_final: 0.5764 (m-10) REVERT: C 185 GLN cc_start: 0.8433 (mt0) cc_final: 0.7732 (mt0) REVERT: C 195 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6291 (t80) outliers start: 9 outliers final: 0 residues processed: 294 average time/residue: 0.1825 time to fit residues: 70.4428 Evaluate side-chains 205 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 195 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4209 > 50: distance: 15 - 23: 3.053 distance: 39 - 43: 10.182 distance: 43 - 44: 5.530 distance: 44 - 45: 6.608 distance: 44 - 47: 6.247 distance: 45 - 50: 13.462 distance: 47 - 48: 15.043 distance: 47 - 49: 17.454 distance: 50 - 51: 22.144 distance: 51 - 52: 13.587 distance: 51 - 54: 20.413 distance: 52 - 53: 24.667 distance: 52 - 58: 26.519 distance: 54 - 55: 16.119 distance: 55 - 56: 10.343 distance: 55 - 57: 15.120 distance: 58 - 59: 9.379 distance: 59 - 60: 32.709 distance: 59 - 62: 45.613 distance: 60 - 64: 10.824 distance: 61 - 82: 58.672 distance: 62 - 63: 26.716 distance: 64 - 65: 27.559 distance: 65 - 66: 29.127 distance: 65 - 68: 49.093 distance: 66 - 67: 20.483 distance: 66 - 72: 41.459 distance: 67 - 90: 39.803 distance: 68 - 69: 40.181 distance: 69 - 70: 41.069 distance: 69 - 71: 57.110 distance: 73 - 74: 41.519 distance: 73 - 76: 42.938 distance: 74 - 75: 50.445 distance: 74 - 78: 50.300 distance: 76 - 77: 43.153 distance: 78 - 79: 40.497 distance: 79 - 80: 39.275 distance: 80 - 82: 69.134 distance: 81 - 104: 20.433 distance: 82 - 83: 38.934 distance: 83 - 84: 20.210 distance: 83 - 86: 31.022 distance: 84 - 85: 42.153 distance: 84 - 90: 38.020 distance: 85 - 112: 32.609 distance: 86 - 87: 8.220 distance: 86 - 88: 53.459 distance: 87 - 89: 11.965 distance: 90 - 91: 24.220 distance: 91 - 92: 23.490 distance: 91 - 94: 41.191 distance: 92 - 93: 49.478 distance: 92 - 98: 10.219 distance: 93 - 119: 29.729 distance: 94 - 95: 15.633 distance: 94 - 96: 14.872 distance: 95 - 97: 37.655 distance: 98 - 99: 53.819 distance: 99 - 100: 43.660 distance: 99 - 102: 25.375 distance: 100 - 101: 45.248 distance: 100 - 104: 27.338 distance: 101 - 125: 31.482 distance: 102 - 103: 33.045 distance: 104 - 105: 18.918 distance: 105 - 106: 35.553 distance: 105 - 108: 42.732 distance: 106 - 107: 20.272 distance: 106 - 112: 22.067 distance: 107 - 129: 32.215 distance: 108 - 109: 4.947 distance: 109 - 110: 30.182 distance: 109 - 111: 31.235