Starting phenix.real_space_refine on Wed Jun 3 17:38:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0l_22601/06_2026/7k0l_22601.map" } resolution = 3.4 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= -0.003 sd= 0.047 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 1 5.49 5 S 44 5.16 5 C 4877 2.51 5 N 1293 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s 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: 7619 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLP': 1, 'VRP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.87, per 1000 atoms: 0.25 Number of scatterers: 7619 At special positions: 0 Unit cell: (95.475, 96.48, 115.575, 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 44 16.00 P 1 15.00 O 1404 8.00 N 1293 7.00 C 4877 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 345.7 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 52.3% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.713A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.501A pdb=" N THR A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.515A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.660A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.704A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.612A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.526A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.570A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.614A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.865A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.528A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 30 through 56 removed outlier: 3.542A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.060A pdb=" N VAL A 94 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.690A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.437A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.995A pdb=" N ILE B 148 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS B 168 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 166 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLN B 152 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N GLY B 164 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.681A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.501A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1137 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: 1.32 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: 1.22 - 1.34: 2465 1.34 - 1.46: 1174 1.46 - 1.58: 4063 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 7775 Sorted by residual: bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.687 1.608 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C2 PLP B 601 " pdb=" N1 PLP B 601 " ideal model delta sigma weight residual 1.325 1.375 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.13e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10204 1.57 - 3.14: 255 3.14 - 4.70: 37 4.70 - 6.27: 4 6.27 - 7.84: 6 Bond angle restraints: 10506 Sorted by residual: angle pdb=" O2P PLP B 601 " pdb=" P PLP B 601 " pdb=" O4P PLP B 601 " ideal model delta sigma weight residual 101.47 109.31 -7.84 3.00e+00 1.11e-01 6.83e+00 angle pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 angle pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" C ASN B 120 " ideal model delta sigma weight residual 113.16 110.18 2.98 1.24e+00 6.50e-01 5.79e+00 angle pdb=" C TYR B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.64e+00 angle pdb=" CA CYS A 133 " pdb=" C CYS A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 115.67 118.55 -2.88 1.23e+00 6.61e-01 5.50e+00 ... (remaining 10501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4222 16.10 - 32.19: 388 32.19 - 48.29: 71 48.29 - 64.38: 10 64.38 - 80.48: 4 Dihedral angle restraints: 4695 sinusoidal: 1911 harmonic: 2784 Sorted by residual: dihedral pdb=" CA THR B 400 " pdb=" C THR B 400 " pdb=" N HIS B 401 " pdb=" CA HIS B 401 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 80.48 -80.48 1 3.00e+01 1.11e-03 8.90e+00 dihedral pdb=" CA ASN B 245 " pdb=" C ASN B 245 " pdb=" N ILE B 246 " pdb=" CA ILE B 246 " ideal model delta harmonic sigma weight residual 180.00 165.15 14.85 0 5.00e+00 4.00e-02 8.82e+00 ... (remaining 4692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 884 0.044 - 0.087: 189 0.087 - 0.131: 82 0.131 - 0.174: 3 0.174 - 0.218: 1 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 177 " pdb=" N ASN B 177 " pdb=" C ASN B 177 " pdb=" CB ASN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1156 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 PLP B 601 " 0.018 2.00e-02 2.50e+03 1.18e-01 3.49e+02 pdb=" C2A PLP B 601 " 0.057 2.00e-02 2.50e+03 pdb=" C3 PLP B 601 " -0.080 2.00e-02 2.50e+03 pdb=" C4 PLP B 601 " -0.115 2.00e-02 2.50e+03 pdb=" C4A PLP B 601 " 0.281 2.00e-02 2.50e+03 pdb=" C5 PLP B 601 " -0.054 2.00e-02 2.50e+03 pdb=" C5A PLP B 601 " -0.091 2.00e-02 2.50e+03 pdb=" C6 PLP B 601 " 0.042 2.00e-02 2.50e+03 pdb=" N1 PLP B 601 " 0.078 2.00e-02 2.50e+03 pdb=" O3 PLP B 601 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 499 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 413 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.031 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 125 2.69 - 3.24: 7377 3.24 - 3.80: 11385 3.80 - 4.35: 14945 4.35 - 4.90: 26010 Nonbonded interactions: 59842 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP B 259 " pdb=" OH TYR B 318 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 401 " pdb=" OD2 ASP A 408 " model vdw 2.246 3.040 nonbonded pdb=" NE2 HIS B 263 " pdb=" O27 VRP B 602 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR A 402 " pdb=" OD1 ASP A 408 " model vdw 2.300 3.040 ... (remaining 59837 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: 3.580 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.130 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.116 7776 Z= 0.237 Angle : 0.616 7.840 10506 Z= 0.362 Chirality : 0.042 0.218 1159 Planarity : 0.005 0.118 1348 Dihedral : 12.492 80.478 2917 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 1.09 (0.27), residues: 958 helix: 1.86 (0.25), residues: 432 sheet: 0.64 (0.48), residues: 124 loop : -0.49 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.023 0.001 TYR A 166 PHE 0.012 0.001 PHE A 209 TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 ( 7775) covalent geometry : angle 0.61552 / 0.36 (10506) hydrogen bonds : bond 0.16052 / 11.93 ( 398) hydrogen bonds : angle 5.93674 / 4.39 ( 1137) Misc. bond : bond 0.11625 / 6.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.388 Fit side-chains REVERT: B 472 MET cc_start: 0.8708 (mmm) cc_final: 0.8463 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0867 time to fit residues: 7.7862 Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081499 restraints weight = 16384.148| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.30 r_work: 0.3083 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7776 Z= 0.147 Angle : 0.507 6.682 10506 Z= 0.274 Chirality : 0.042 0.146 1159 Planarity : 0.004 0.055 1348 Dihedral : 4.654 34.406 1101 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.15 % 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: 1.19 (0.27), residues: 958 helix: 1.95 (0.25), residues: 445 sheet: 0.57 (0.46), residues: 131 loop : -0.50 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.025 0.001 TYR A 166 PHE 0.012 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7775) covalent geometry : angle 0.50671 / 0.27 (10506) hydrogen bonds : bond 0.04878 / 3.40 ( 398) hydrogen bonds : angle 4.73300 / 3.49 ( 1137) Misc. bond : bond 0.00120 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.313 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0794 time to fit residues: 6.4880 Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082710 restraints weight = 16215.289| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.29 r_work: 0.3105 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7776 Z= 0.117 Angle : 0.473 6.645 10506 Z= 0.254 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.052 1348 Dihedral : 4.266 35.459 1101 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.87 % Allowed : 5.98 % Favored : 93.15 % 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: 1.24 (0.27), residues: 958 helix: 2.05 (0.25), residues: 445 sheet: 0.43 (0.45), residues: 129 loop : -0.49 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.019 0.001 TYR A 166 PHE 0.012 0.001 PHE B 498 TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7775) covalent geometry : angle 0.47290 / 0.25 (10506) hydrogen bonds : bond 0.04079 / 2.78 ( 398) hydrogen bonds : angle 4.45623 / 3.28 ( 1137) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.217 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.0747 time to fit residues: 6.8069 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 68.8961 > 50: distance: 43 - 190: 33.723 distance: 54 - 193: 15.389 distance: 57 - 205: 3.169 distance: 98 - 103: 21.426 distance: 103 - 104: 14.645 distance: 104 - 105: 28.132 distance: 105 - 106: 29.221 distance: 105 - 114: 26.745 distance: 107 - 108: 10.298 distance: 108 - 109: 29.106 distance: 109 - 110: 9.825 distance: 110 - 111: 15.360 distance: 111 - 112: 14.664 distance: 111 - 113: 23.978 distance: 114 - 115: 24.919 distance: 115 - 116: 6.205 distance: 115 - 118: 48.077 distance: 116 - 117: 18.736 distance: 116 - 121: 22.383 distance: 118 - 119: 32.355 distance: 118 - 120: 35.112 distance: 121 - 122: 35.051 distance: 122 - 123: 47.409 distance: 122 - 125: 49.504 distance: 123 - 124: 54.727 distance: 123 - 132: 54.946 distance: 125 - 126: 48.165 distance: 128 - 129: 22.047 distance: 129 - 130: 20.252 distance: 129 - 131: 43.429 distance: 132 - 133: 46.990 distance: 133 - 134: 52.670 distance: 133 - 136: 41.337 distance: 134 - 135: 29.516 distance: 134 - 143: 62.656 distance: 136 - 137: 20.173 distance: 137 - 138: 33.155 distance: 138 - 139: 23.350 distance: 139 - 140: 15.143 distance: 140 - 141: 35.076 distance: 140 - 142: 41.852 distance: 143 - 144: 56.571 distance: 143 - 149: 6.000 distance: 144 - 145: 26.997 distance: 145 - 146: 31.315 distance: 145 - 150: 25.521 distance: 147 - 148: 40.237 distance: 148 - 149: 32.195 distance: 150 - 151: 13.035 distance: 151 - 152: 37.628 distance: 151 - 154: 41.783 distance: 152 - 153: 34.232 distance: 152 - 164: 22.419 distance: 155 - 156: 9.899 distance: 155 - 157: 10.615 distance: 156 - 158: 4.382 distance: 157 - 159: 9.631 distance: 157 - 160: 19.286 distance: 158 - 159: 11.951 distance: 159 - 161: 10.671 distance: 160 - 162: 3.636 distance: 161 - 163: 10.499 distance: 162 - 163: 5.237 distance: 164 - 165: 26.979 distance: 165 - 166: 47.089 distance: 165 - 168: 3.996 distance: 166 - 167: 34.793 distance: 166 - 173: 39.478 distance: 168 - 169: 21.354 distance: 169 - 170: 18.096 distance: 170 - 171: 11.902 distance: 171 - 172: 31.656 distance: 173 - 174: 9.689 distance: 174 - 175: 14.415 distance: 174 - 177: 22.390 distance: 175 - 182: 43.477 distance: 177 - 178: 15.370 distance: 178 - 179: 7.805 distance: 179 - 180: 12.013 distance: 180 - 181: 12.695 distance: 182 - 183: 35.484 distance: 183 - 184: 56.586 distance: 183 - 186: 40.343 distance: 184 - 185: 57.682 distance: 184 - 190: 55.442 distance: 186 - 187: 11.033 distance: 187 - 189: 9.280 distance: 190 - 191: 44.379 distance: 191 - 192: 19.975 distance: 191 - 194: 18.241 distance: 192 - 193: 24.459 distance: 192 - 198: 26.677 distance: 194 - 195: 27.921 distance: 195 - 196: 14.403 distance: 195 - 197: 15.283