Starting phenix.real_space_refine on Fri Aug 22 22:15:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.map" model { file = "/net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uve_42617/08_2025/8uve_42617.cif" } resolution = 2.6 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= -0.001 sd= 0.059 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 Na 2 4.78 5 C 5730 2.51 5 N 1249 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8373 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3887 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 33, 'TRANS': 463} Chain breaks: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 219 Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 256 Unusual residues: {' NA': 1, '3PE': 2, 'C14': 3, 'CLR': 4, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8373 At special positions: 0 Unit cell: (88.275, 106.425, 84.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 2 15.00 Na 2 11.00 O 1339 8.00 N 1249 7.00 C 5730 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=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 322.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.566A pdb=" N ALA B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.735A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.836A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.539A pdb=" N PHE B 86 " --> pdb=" O PRO B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.581A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.632A pdb=" N ARG B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 225 through 246 removed outlier: 4.686A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.861A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.547A pdb=" N GLY B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.660A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.093A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 removed outlier: 3.573A pdb=" N ILE B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 502 Proline residue: B 493 - end of helix removed outlier: 3.621A pdb=" N ILE B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.008A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 14 through 28 Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.972A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.891A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.552A pdb=" N PHE A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.577A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.710A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.973A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.853A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.004A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.822A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.228A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 502 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 506 through 517 Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.035A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 532 hydrogen bonds defined for protein. 1578 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: 1.45 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1240 1.32 - 1.44: 2204 1.44 - 1.57: 5084 1.57 - 1.69: 4 1.69 - 1.81: 88 Bond restraints: 8620 Sorted by residual: bond pdb=" C11 3PE A 705 " pdb=" O13 3PE A 705 " ideal model delta sigma weight residual 1.408 1.457 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C1 3PE A 709 " pdb=" O11 3PE A 709 " ideal model delta sigma weight residual 1.409 1.457 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C11 3PE A 709 " pdb=" O13 3PE A 709 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" O13 3PE A 709 " pdb=" P 3PE A 709 " ideal model delta sigma weight residual 1.654 1.607 0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" O13 3PE A 705 " pdb=" P 3PE A 705 " ideal model delta sigma weight residual 1.654 1.608 0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 8615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11556 2.12 - 4.24: 168 4.24 - 6.36: 31 6.36 - 8.48: 2 8.48 - 10.60: 1 Bond angle restraints: 11758 Sorted by residual: angle pdb=" CB MET B 131 " pdb=" CG MET B 131 " pdb=" SD MET B 131 " ideal model delta sigma weight residual 112.70 102.10 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C TYR B 85 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " ideal model delta sigma weight residual 122.62 118.63 3.99 1.63e+00 3.76e-01 6.01e+00 angle pdb=" C ILE B 364 " pdb=" CA ILE B 364 " pdb=" CB ILE B 364 " ideal model delta sigma weight residual 110.13 112.22 -2.09 9.70e-01 1.06e+00 4.65e+00 angle pdb=" C VAL B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 119.84 122.47 -2.63 1.25e+00 6.40e-01 4.43e+00 angle pdb=" C VAL A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.84 122.46 -2.62 1.25e+00 6.40e-01 4.40e+00 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.30: 5247 24.30 - 48.60: 254 48.60 - 72.90: 39 72.90 - 97.19: 7 97.19 - 121.49: 7 Dihedral angle restraints: 5554 sinusoidal: 2644 harmonic: 2910 Sorted by residual: dihedral pdb=" CA PHE A 363 " pdb=" C PHE A 363 " pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N LEU A 87 " pdb=" CA LEU A 87 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C10 CLR A 710 " pdb=" C1 CLR A 710 " pdb=" C2 CLR A 710 " pdb=" C3 CLR A 710 " ideal model delta sinusoidal sigma weight residual -56.83 64.66 -121.49 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 5551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 993 0.039 - 0.079: 295 0.079 - 0.118: 81 0.118 - 0.157: 15 0.157 - 0.196: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C2 3PE A 705 " pdb=" C1 3PE A 705 " pdb=" C3 3PE A 705 " pdb=" O21 3PE A 705 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" C2 3PE A 709 " pdb=" C1 3PE A 709 " pdb=" C3 3PE A 709 " pdb=" O21 3PE A 709 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET B 131 " pdb=" N MET B 131 " pdb=" C MET B 131 " pdb=" CB MET B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1383 not shown) Planarity restraints: 1361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 152 " 0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 153 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 528 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO B 529 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 529 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 529 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 86 " 0.020 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE B 86 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 86 " 0.002 2.00e-02 2.50e+03 ... (remaining 1358 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1480 2.76 - 3.30: 8227 3.30 - 3.83: 14518 3.83 - 4.37: 17236 4.37 - 4.90: 29649 Nonbonded interactions: 71110 Sorted by model distance: nonbonded pdb=" O ALA B 63 " pdb=" OH TYR B 85 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU B 480 " pdb=" N MET B 522 " model vdw 2.257 3.120 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 240 " pdb=" O PHE A 521 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" O PHE B 521 " model vdw 2.275 3.040 ... (remaining 71105 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 219 or resid 225 through 303 or resid 319 throug \ h 576 or resid 701 through 704 or resid 706 through 708)) selection = (chain 'B' and (resid 6 through 704 or resid 706 through 708)) } 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: 3.310 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:9.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 0.049 8620 Z= 0.182 Angle : 0.623 10.604 11758 Z= 0.293 Chirality : 0.041 0.196 1386 Planarity : 0.006 0.082 1361 Dihedral : 14.477 121.493 3662 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 2.23 (0.28), residues: 998 helix: 1.88 (0.20), residues: 765 sheet: None (None), residues: 0 loop : 0.29 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 228 TYR 0.017 0.001 TYR B 508 PHE 0.041 0.001 PHE B 86 TRP 0.037 0.002 TRP B 231 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8620) covalent geometry : angle 0.62268 (11758) hydrogen bonds : bond 0.11269 ( 532) hydrogen bonds : angle 4.78880 ( 1578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.314 Fit side-chains REVERT: B 118 MET cc_start: 0.8172 (mtt) cc_final: 0.7870 (mtm) REVERT: B 231 TRP cc_start: 0.5846 (m100) cc_final: 0.5072 (m-90) REVERT: B 508 TYR cc_start: 0.7499 (t80) cc_final: 0.7045 (t80) REVERT: A 228 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7047 (mtm110) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.4979 time to fit residues: 75.4793 Evaluate side-chains 118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 HIS A 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108841 restraints weight = 10997.525| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.04 r_work: 0.3295 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8620 Z= 0.148 Angle : 0.602 8.230 11758 Z= 0.288 Chirality : 0.041 0.164 1386 Planarity : 0.006 0.071 1361 Dihedral : 9.090 85.152 1866 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.36 % Allowed : 8.25 % Favored : 89.39 % 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 aren not related in a simple way. whole: 2.32 (0.28), residues: 998 helix: 1.89 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.45 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 329 TYR 0.015 0.001 TYR B 508 PHE 0.020 0.001 PHE B 86 TRP 0.017 0.001 TRP B 231 HIS 0.008 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8620) covalent geometry : angle 0.60230 (11758) hydrogen bonds : bond 0.03835 ( 532) hydrogen bonds : angle 3.99086 ( 1578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.335 Fit side-chains REVERT: B 413 GLU cc_start: 0.7527 (tp30) cc_final: 0.7241 (tp30) REVERT: B 508 TYR cc_start: 0.7461 (t80) cc_final: 0.6939 (t80) REVERT: A 228 ARG cc_start: 0.7370 (mtm180) cc_final: 0.7138 (mtm110) REVERT: A 572 GLN cc_start: 0.7920 (mm110) cc_final: 0.7588 (mm110) outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.4518 time to fit residues: 65.6057 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 99 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.146868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109590 restraints weight = 10875.971| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.03 r_work: 0.3311 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.121 Angle : 0.544 6.653 11758 Z= 0.264 Chirality : 0.040 0.193 1386 Planarity : 0.006 0.070 1361 Dihedral : 8.675 87.410 1866 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.48 % Allowed : 10.14 % Favored : 87.38 % 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 aren not related in a simple way. whole: 2.49 (0.28), residues: 998 helix: 2.00 (0.19), residues: 773 sheet: None (None), residues: 0 loop : 0.57 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 329 TYR 0.011 0.001 TYR B 508 PHE 0.016 0.001 PHE A 352 TRP 0.018 0.001 TRP B 231 HIS 0.007 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8620) covalent geometry : angle 0.54421 (11758) hydrogen bonds : bond 0.03423 ( 532) hydrogen bonds : angle 3.79866 ( 1578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.342 Fit side-chains REVERT: B 413 GLU cc_start: 0.7516 (tp30) cc_final: 0.7203 (tp30) REVERT: B 508 TYR cc_start: 0.7460 (t80) cc_final: 0.6881 (t80) REVERT: A 228 ARG cc_start: 0.7330 (mtm180) cc_final: 0.7093 (mtm110) REVERT: A 445 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 21 outliers final: 9 residues processed: 140 average time/residue: 0.4530 time to fit residues: 68.6893 Evaluate side-chains 126 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4317 > 50: distance: 59 - 60: 4.626 distance: 60 - 61: 7.943 distance: 60 - 63: 4.656 distance: 61 - 62: 14.105 distance: 61 - 68: 7.575 distance: 63 - 64: 14.288 distance: 64 - 65: 10.493 distance: 65 - 66: 7.157 distance: 65 - 67: 15.638 distance: 68 - 69: 4.501 distance: 69 - 70: 20.528 distance: 69 - 72: 17.006 distance: 70 - 71: 12.993 distance: 70 - 73: 12.639 distance: 73 - 74: 9.294 distance: 74 - 75: 4.558 distance: 74 - 77: 6.344 distance: 75 - 76: 7.822 distance: 75 - 81: 13.289 distance: 78 - 79: 17.446 distance: 78 - 80: 15.381 distance: 81 - 87: 4.883 distance: 82 - 83: 4.590 distance: 82 - 85: 7.239 distance: 83 - 84: 7.762 distance: 83 - 88: 6.177 distance: 84 - 109: 25.903 distance: 85 - 86: 8.697 distance: 86 - 87: 10.201 distance: 88 - 89: 7.209 distance: 89 - 90: 8.542 distance: 89 - 92: 5.240 distance: 90 - 91: 3.035 distance: 90 - 96: 4.849 distance: 91 - 116: 12.245 distance: 92 - 93: 13.131 distance: 93 - 94: 5.321 distance: 93 - 95: 6.872 distance: 96 - 97: 10.169 distance: 97 - 98: 5.589 distance: 97 - 100: 17.858 distance: 98 - 102: 5.534 distance: 99 - 121: 5.546 distance: 100 - 101: 18.131 distance: 102 - 103: 6.351 distance: 103 - 104: 9.159 distance: 103 - 106: 11.152 distance: 104 - 105: 24.291 distance: 104 - 109: 32.133 distance: 106 - 107: 16.758 distance: 106 - 108: 17.400 distance: 109 - 110: 6.362 distance: 110 - 111: 21.360 distance: 110 - 113: 16.188 distance: 111 - 112: 12.610 distance: 111 - 116: 8.712 distance: 113 - 114: 8.470 distance: 113 - 115: 19.503 distance: 116 - 117: 9.942 distance: 117 - 118: 5.077 distance: 117 - 120: 3.559 distance: 118 - 119: 4.174 distance: 118 - 121: 4.463 distance: 121 - 122: 7.583 distance: 122 - 123: 4.107 distance: 122 - 125: 9.381 distance: 123 - 124: 3.963 distance: 126 - 127: 8.940 distance: 126 - 128: 11.327