Starting phenix.real_space_refine on Wed Jun 3 11:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.cif Found real_map, /net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21aq_67524/06_2026/21aq_67524.map" } resolution = 2.97 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= 0.029 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 2664 2.51 5 N 725 2.21 5 O 854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 813 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2424 Classifications: {'peptide': 315} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.35, per 1000 atoms: 0.32 Number of scatterers: 4276 At special positions: 0 Unit cell: (58.9, 78.85, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 854 8.00 N 725 7.00 C 2664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 156 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 327 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 266 " distance=2.05 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 305 " distance=2.06 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 303 " distance=2.04 Simple disulfide: pdb=" SG CYS H 274 " - pdb=" SG CYS H 280 " distance=2.03 Simple disulfide: pdb=" SG CYS H 287 " - pdb=" SG CYS H 292 " 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 7 " " MAN C 4 " - " MAN C 5 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN H 63 " " NAG D 1 " - " ASN H 33 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 190.1 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 14 sheets defined 17.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.874A pdb=" N THR A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.569A pdb=" N SER B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.716A pdb=" N GLU B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 53 Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.552A pdb=" N GLN H 79 " --> pdb=" O GLY H 76 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 80 " --> pdb=" O ARG H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 80' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.697A pdb=" N TRP H 103 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 270 through 278 removed outlier: 3.505A pdb=" N THR H 276 " --> pdb=" O LYS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.094A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.184A pdb=" N HIS A 112 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'H' and resid 70 through 71 removed outlier: 6.712A pdb=" N TYR H 70 " --> pdb=" O LEU H 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.530A pdb=" N PHE H 129 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE H 175 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU H 131 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 147 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.509A pdb=" N ASP H 177 " --> pdb=" O PHE H 330 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS H 207 " --> pdb=" O THR H 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.509A pdb=" N ASP H 177 " --> pdb=" O PHE H 330 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS H 327 " --> pdb=" O ASP H 231 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA H 228 " --> pdb=" O MET H 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 218 through 219 removed outlier: 7.353A pdb=" N GLY H 218 " --> pdb=" O ASN H 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AB5, first strand: chain 'H' and resid 256 through 257 157 hydrogen bonds defined for protein. 384 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: 0.60 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 1391 1.36 - 1.49: 1173 1.49 - 1.62: 1764 1.62 - 1.75: 1 1.75 - 1.88: 45 Bond restraints: 4374 Sorted by residual: bond pdb=" CB PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" CB CYS H 305 " pdb=" SG CYS H 305 " ideal model delta sigma weight residual 1.808 1.883 -0.075 3.30e-02 9.18e+02 5.21e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.54e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 4369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 5861 2.78 - 5.55: 47 5.55 - 8.33: 10 8.33 - 11.11: 0 11.11 - 13.89: 1 Bond angle restraints: 5919 Sorted by residual: angle pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 112.00 98.11 13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" N PRO A 14 " pdb=" CD PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 103.20 95.53 7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" N CYS H 258 " pdb=" CA CYS H 258 " pdb=" C CYS H 258 " ideal model delta sigma weight residual 108.74 113.12 -4.38 1.38e+00 5.25e-01 1.01e+01 angle pdb=" CA PRO A 14 " pdb=" CB PRO A 14 " pdb=" CG PRO A 14 " ideal model delta sigma weight residual 104.50 98.49 6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " ideal model delta sigma weight residual 114.40 121.59 -7.19 2.30e+00 1.89e-01 9.77e+00 ... (remaining 5914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 2565 21.59 - 43.19: 135 43.19 - 64.78: 24 64.78 - 86.37: 9 86.37 - 107.96: 5 Dihedral angle restraints: 2738 sinusoidal: 1200 harmonic: 1538 Sorted by residual: dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 303 " pdb=" CB CYS H 303 " ideal model delta sinusoidal sigma weight residual -86.00 -165.55 79.55 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " pdb=" SG CYS H 305 " pdb=" CB CYS H 305 " ideal model delta sinusoidal sigma weight residual 93.00 35.06 57.94 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS H 274 " pdb=" SG CYS H 274 " pdb=" SG CYS H 280 " pdb=" CB CYS H 280 " ideal model delta sinusoidal sigma weight residual 93.00 148.91 -55.91 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 2735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 521 0.054 - 0.108: 104 0.108 - 0.162: 29 0.162 - 0.216: 0 0.216 - 0.270: 1 Chirality restraints: 655 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN H 33 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA CYS H 258 " pdb=" N CYS H 258 " pdb=" C CYS H 258 " pdb=" CB CYS H 258 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 652 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 13 " 0.083 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 14 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 119 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO H 120 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 120 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 120 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 14 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C PRO A 14 " -0.027 2.00e-02 2.50e+03 pdb=" O PRO A 14 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY A 15 " 0.009 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 631 2.77 - 3.30: 3697 3.30 - 3.83: 6784 3.83 - 4.37: 8042 4.37 - 4.90: 14539 Nonbonded interactions: 33693 Sorted by model distance: nonbonded pdb=" OD2 ASP B 91 " pdb=" OG1 THR B 94 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU H 201 " pdb=" OH TYR H 318 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR B 35 " pdb=" OE1 GLN B 88 " model vdw 2.292 3.040 nonbonded pdb=" O GLU H 268 " pdb=" OG SER H 269 " model vdw 2.323 3.040 nonbonded pdb=" NH1 ARG H 77 " pdb=" OD2 ASP H 100 " model vdw 2.349 3.120 ... (remaining 33688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.240 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.004 0.170 4394 Z= 0.174 Angle : 0.708 13.886 5968 Z= 0.360 Chirality : 0.048 0.270 655 Planarity : 0.006 0.115 755 Dihedral : 14.189 107.964 1731 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.35), residues: 538 helix: 0.17 (0.65), residues: 69 sheet: 0.32 (0.44), residues: 146 loop : -0.79 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.009 0.001 TYR A 80 PHE 0.013 0.001 PHE H 130 TRP 0.008 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 ( 4374) covalent geometry : angle 0.67807 / 0.35 ( 5919) SS BOND : bond 0.00978 / 0.48 ( 11) SS BOND : angle 2.31742 / 1.53 ( 22) hydrogen bonds : bond 0.26491 / 18.80 ( 147) hydrogen bonds : angle 8.78356 / 6.36 ( 384) link_ALPHA1-3 : bond 0.00422 / 0.21 ( 2) link_ALPHA1-3 : angle 1.55676 / 0.76 ( 6) link_ALPHA1-6 : bond 0.00343 / 0.17 ( 2) link_ALPHA1-6 : angle 1.54420 / 0.76 ( 6) link_BETA1-4 : bond 0.00650 / 0.33 ( 3) link_BETA1-4 : angle 3.39219 / 1.55 ( 9) link_NAG-ASN : bond 0.00376 / 0.20 ( 2) link_NAG-ASN : angle 1.86162 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.7213 time to fit residues: 54.1369 Evaluate side-chains 52 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109951 restraints weight = 5065.316| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.14 r_work: 0.3138 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4394 Z= 0.140 Angle : 0.619 8.402 5968 Z= 0.322 Chirality : 0.047 0.207 655 Planarity : 0.005 0.043 755 Dihedral : 10.404 79.770 773 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 9.15 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.27 (0.36), residues: 538 helix: 0.29 (0.64), residues: 70 sheet: 0.67 (0.43), residues: 154 loop : -0.72 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.008 0.001 TYR H 83 PHE 0.013 0.002 PHE H 130 TRP 0.014 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4374) covalent geometry : angle 0.58530 / 0.31 ( 5919) SS BOND : bond 0.00996 / 0.50 ( 11) SS BOND : angle 2.14301 / 1.35 ( 22) hydrogen bonds : bond 0.04653 / 3.22 ( 147) hydrogen bonds : angle 5.86237 / 4.26 ( 384) link_ALPHA1-3 : bond 0.00793 / 0.40 ( 2) link_ALPHA1-3 : angle 1.77438 / 0.90 ( 6) link_ALPHA1-6 : bond 0.00391 / 0.20 ( 2) link_ALPHA1-6 : angle 1.83451 / 0.91 ( 6) link_BETA1-4 : bond 0.00411 / 0.21 ( 3) link_BETA1-4 : angle 3.26688 / 1.51 ( 9) link_NAG-ASN : bond 0.00260 / 0.14 ( 2) link_NAG-ASN : angle 2.02559 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.173 Fit side-chains REVERT: H 79 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8923 (mm110) outliers start: 7 outliers final: 2 residues processed: 57 average time/residue: 0.6626 time to fit residues: 38.9315 Evaluate side-chains 53 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 253 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/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-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5015 > 50: distance: 52 - 57: 4.000 distance: 57 - 58: 25.066 distance: 58 - 59: 8.967 distance: 58 - 61: 29.144 distance: 59 - 60: 46.296 distance: 59 - 65: 31.289 distance: 61 - 62: 42.805 distance: 62 - 63: 16.039 distance: 65 - 66: 31.461 distance: 66 - 67: 20.119 distance: 66 - 69: 34.870 distance: 67 - 68: 15.256 distance: 67 - 71: 12.537 distance: 69 - 70: 9.893 distance: 71 - 72: 20.887 distance: 72 - 73: 19.295 distance: 72 - 75: 31.614 distance: 73 - 74: 7.182 distance: 73 - 78: 34.403 distance: 75 - 76: 5.106 distance: 75 - 77: 26.586 distance: 78 - 79: 28.360 distance: 79 - 80: 15.846 distance: 79 - 82: 10.984 distance: 80 - 81: 30.578 distance: 80 - 89: 10.186 distance: 82 - 83: 15.296 distance: 83 - 84: 21.268 distance: 84 - 85: 20.603 distance: 85 - 86: 17.538 distance: 86 - 87: 12.748 distance: 86 - 88: 18.280 distance: 89 - 90: 5.776 distance: 89 - 95: 8.820 distance: 90 - 91: 11.394 distance: 90 - 93: 8.744 distance: 91 - 92: 34.621 distance: 91 - 96: 12.578 distance: 93 - 94: 21.630 distance: 94 - 95: 26.123 distance: 96 - 97: 12.721 distance: 97 - 98: 29.268 distance: 97 - 100: 16.536 distance: 98 - 99: 11.245 distance: 98 - 102: 20.325 distance: 100 - 101: 22.060 distance: 102 - 103: 36.844 distance: 103 - 104: 17.541 distance: 103 - 106: 18.408 distance: 104 - 105: 3.893 distance: 104 - 113: 13.092 distance: 106 - 107: 41.380 distance: 107 - 108: 20.612 distance: 108 - 109: 3.835 distance: 109 - 110: 12.187 distance: 110 - 111: 11.587 distance: 110 - 112: 9.679 distance: 113 - 114: 26.694 distance: 114 - 115: 19.741 distance: 114 - 117: 11.546 distance: 115 - 116: 15.838 distance: 115 - 121: 14.767 distance: 117 - 118: 17.692 distance: 117 - 119: 14.234 distance: 118 - 120: 16.948 distance: 121 - 122: 11.551 distance: 121 - 127: 42.239 distance: 122 - 123: 21.133 distance: 122 - 125: 8.623 distance: 123 - 124: 8.571 distance: 123 - 128: 38.361 distance: 125 - 126: 42.654 distance: 126 - 127: 26.298 distance: 128 - 129: 9.713 distance: 129 - 130: 13.334 distance: 129 - 132: 15.498 distance: 130 - 131: 11.377 distance: 130 - 137: 7.349 distance: 132 - 133: 11.978 distance: 134 - 135: 28.456 distance: 134 - 136: 3.358