Starting phenix.real_space_refine on Tue Feb 3 19:42:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxp_61871/02_2026/9jxp_61871.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 32 5.16 5 C 4326 2.51 5 N 1024 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6430 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3215 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 12, 'TRANS': 372} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 1.94, per 1000 atoms: 0.30 Number of scatterers: 6430 At special positions: 0 Unit cell: (119.215, 66.465, 75.96, 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 32 16.00 O 1048 8.00 N 1024 7.00 C 4326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 251.3 milliseconds 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 231 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.371A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.364A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.790A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.184A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.913A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 470 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 473 through 503 removed outlier: 3.636A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.622A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 570 removed outlier: 3.818A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 removed outlier: 3.558A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 Proline residue: A 598 - end of helix removed outlier: 4.487A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.371A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.364A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.791A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 4.185A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.913A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 470 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 503 removed outlier: 3.636A pdb=" N LEU B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.622A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 570 removed outlier: 3.818A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 581 removed outlier: 3.558A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 619 Proline residue: B 598 - end of helix removed outlier: 4.486A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1290 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: 0.67 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1888 1.34 - 1.46: 1801 1.46 - 1.58: 2913 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 6646 Sorted by residual: bond pdb=" C GLY B 621 " pdb=" N GLU B 622 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.25e-02 6.40e+03 5.96e+00 bond pdb=" C GLY A 621 " pdb=" N GLU A 622 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.25e-02 6.40e+03 5.55e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB VAL A 246 " pdb=" CG1 VAL A 246 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.65e+00 bond pdb=" CA GLU B 622 " pdb=" C GLU B 622 " ideal model delta sigma weight residual 1.530 1.518 0.011 1.10e-02 8.26e+03 1.06e+00 ... (remaining 6641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8634 1.52 - 3.03: 332 3.03 - 4.55: 52 4.55 - 6.07: 18 6.07 - 7.58: 6 Bond angle restraints: 9042 Sorted by residual: angle pdb=" N GLU A 622 " pdb=" CA GLU A 622 " pdb=" CB GLU A 622 " ideal model delta sigma weight residual 110.60 104.20 6.40 1.51e+00 4.39e-01 1.80e+01 angle pdb=" N GLU B 622 " pdb=" CA GLU B 622 " pdb=" CB GLU B 622 " ideal model delta sigma weight residual 110.60 104.25 6.35 1.51e+00 4.39e-01 1.77e+01 angle pdb=" CA GLU B 622 " pdb=" C GLU B 622 " pdb=" O GLU B 622 " ideal model delta sigma weight residual 122.64 117.85 4.79 1.25e+00 6.40e-01 1.47e+01 angle pdb=" CA GLU A 622 " pdb=" C GLU A 622 " pdb=" O GLU A 622 " ideal model delta sigma weight residual 122.64 117.93 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N HIS A 441 " pdb=" CA HIS A 441 " pdb=" C HIS A 441 " ideal model delta sigma weight residual 113.28 108.74 4.54 1.57e+00 4.06e-01 8.36e+00 ... (remaining 9037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3363 17.89 - 35.79: 314 35.79 - 53.68: 69 53.68 - 71.57: 4 71.57 - 89.47: 4 Dihedral angle restraints: 3754 sinusoidal: 1482 harmonic: 2272 Sorted by residual: dihedral pdb=" CA LEU B 569 " pdb=" C LEU B 569 " pdb=" N LEU B 570 " pdb=" CA LEU B 570 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 569 " pdb=" C LEU A 569 " pdb=" N LEU A 570 " pdb=" CA LEU A 570 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA CYS B 440 " pdb=" C CYS B 440 " pdb=" N HIS B 441 " pdb=" CA HIS B 441 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 528 0.029 - 0.058: 307 0.058 - 0.087: 117 0.087 - 0.116: 34 0.116 - 0.145: 4 Chirality restraints: 990 Sorted by residual: chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA GLU A 622 " pdb=" N GLU A 622 " pdb=" C GLU A 622 " pdb=" CB GLU A 622 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 987 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 609 " -0.018 2.00e-02 2.50e+03 1.48e-02 3.81e+00 pdb=" CG PHE B 609 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 609 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 609 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 609 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 609 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 609 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 609 " -0.018 2.00e-02 2.50e+03 1.46e-02 3.73e+00 pdb=" CG PHE A 609 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 609 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 609 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 609 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 609 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 609 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 337 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 338 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.025 5.00e-02 4.00e+02 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 70 2.65 - 3.21: 6366 3.21 - 3.78: 10252 3.78 - 4.34: 13112 4.34 - 4.90: 21682 Nonbonded interactions: 51482 Sorted by model distance: nonbonded pdb=" OE2 GLU B 318 " pdb=" OH TYR B 367 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 318 " pdb=" OH TYR A 367 " model vdw 2.088 3.040 nonbonded pdb=" OH TYR B 272 " pdb=" OG SER B 330 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 272 " pdb=" OG SER A 330 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 270 " pdb=" OD1 ASP A 590 " model vdw 2.281 3.120 ... (remaining 51477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.580 Find NCS groups from input model: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.005 0.064 6648 Z= 0.228 Angle : 0.715 7.584 9046 Z= 0.415 Chirality : 0.041 0.145 990 Planarity : 0.004 0.046 1096 Dihedral : 14.250 89.465 2284 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.27), residues: 762 helix: -0.76 (0.19), residues: 552 sheet: None (None), residues: 0 loop : -4.25 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 611 TYR 0.026 0.002 TYR B 518 PHE 0.034 0.002 PHE B 609 TRP 0.006 0.001 TRP A 457 HIS 0.010 0.002 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 6646) covalent geometry : angle 0.71401 ( 9042) SS BOND : bond 0.00230 ( 2) SS BOND : angle 1.72681 ( 4) hydrogen bonds : bond 0.10453 ( 432) hydrogen bonds : angle 5.41007 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.187 Fit side-chains REVERT: A 445 TYR cc_start: 0.8013 (m-80) cc_final: 0.7768 (m-80) REVERT: A 468 ARG cc_start: 0.7488 (ttp80) cc_final: 0.6609 (ttm170) REVERT: A 565 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 579 ILE cc_start: 0.8612 (tp) cc_final: 0.8296 (tp) REVERT: A 615 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7515 (tp30) REVERT: B 445 TYR cc_start: 0.8012 (m-80) cc_final: 0.7748 (m-80) REVERT: B 468 ARG cc_start: 0.7446 (ttp80) cc_final: 0.6544 (ttm170) REVERT: B 508 MET cc_start: 0.7993 (tpt) cc_final: 0.7710 (tpp) REVERT: B 565 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 579 ILE cc_start: 0.8584 (tp) cc_final: 0.8264 (tp) REVERT: B 615 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7451 (tp30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0623 time to fit residues: 9.4041 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.0060 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 476 HIS A 618 ASN A 619 ASN B 452 GLN B 476 HIS B 618 ASN B 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120864 restraints weight = 6953.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125005 restraints weight = 4350.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127748 restraints weight = 3319.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129350 restraints weight = 2831.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130508 restraints weight = 2572.162| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6648 Z= 0.152 Angle : 0.602 8.928 9046 Z= 0.310 Chirality : 0.039 0.131 990 Planarity : 0.004 0.043 1096 Dihedral : 4.274 18.202 848 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.61 % Allowed : 16.08 % Favored : 82.31 % 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: -0.87 (0.31), residues: 762 helix: 0.57 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -3.83 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.017 0.001 TYR A 518 PHE 0.012 0.001 PHE B 609 TRP 0.005 0.001 TRP A 266 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6646) covalent geometry : angle 0.60173 ( 9042) SS BOND : bond 0.00022 ( 2) SS BOND : angle 1.34487 ( 4) hydrogen bonds : bond 0.04398 ( 432) hydrogen bonds : angle 4.32531 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.158 Fit side-chains REVERT: A 270 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7821 (mtm-85) REVERT: A 445 TYR cc_start: 0.8320 (m-80) cc_final: 0.7969 (m-80) REVERT: A 468 ARG cc_start: 0.7423 (ttp80) cc_final: 0.6403 (ttm170) REVERT: A 487 PHE cc_start: 0.7031 (m-10) cc_final: 0.6668 (m-10) REVERT: A 550 GLU cc_start: 0.8229 (pm20) cc_final: 0.7790 (pm20) REVERT: A 565 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 579 ILE cc_start: 0.8222 (tp) cc_final: 0.7922 (tp) REVERT: A 615 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7203 (tp30) REVERT: B 270 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7803 (mtm-85) REVERT: B 445 TYR cc_start: 0.8316 (m-80) cc_final: 0.7961 (m-80) REVERT: B 468 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6364 (ttm170) REVERT: B 487 PHE cc_start: 0.6898 (m-10) cc_final: 0.6534 (m-10) REVERT: B 508 MET cc_start: 0.7864 (tpt) cc_final: 0.7642 (tpp) REVERT: B 550 GLU cc_start: 0.8230 (pm20) cc_final: 0.7752 (pm20) REVERT: B 565 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 579 ILE cc_start: 0.8233 (tp) cc_final: 0.7922 (tp) REVERT: B 615 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7149 (tp30) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 0.0689 time to fit residues: 9.3454 Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.166528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121239 restraints weight = 6884.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125326 restraints weight = 4328.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127991 restraints weight = 3312.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129563 restraints weight = 2815.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130804 restraints weight = 2555.646| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6648 Z= 0.149 Angle : 0.575 7.561 9046 Z= 0.297 Chirality : 0.038 0.135 990 Planarity : 0.004 0.042 1096 Dihedral : 4.061 16.779 848 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.36 % Allowed : 18.57 % Favored : 78.07 % 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: -0.03 (0.32), residues: 762 helix: 1.19 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -3.50 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.014 0.001 TYR B 518 PHE 0.016 0.001 PHE B 609 TRP 0.005 0.001 TRP A 457 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6646) covalent geometry : angle 0.57391 ( 9042) SS BOND : bond 0.00070 ( 2) SS BOND : angle 1.41763 ( 4) hydrogen bonds : bond 0.04284 ( 432) hydrogen bonds : angle 4.05799 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1524 Ramachandran restraints generated. 762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.163 Fit side-chains REVERT: A 270 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7899 (mtm-85) REVERT: A 445 TYR cc_start: 0.8256 (m-80) cc_final: 0.7902 (m-80) REVERT: A 468 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6363 (ttm170) REVERT: A 487 PHE cc_start: 0.7097 (m-10) cc_final: 0.6652 (m-10) REVERT: A 550 GLU cc_start: 0.8265 (pm20) cc_final: 0.7904 (pm20) REVERT: A 565 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 579 ILE cc_start: 0.8083 (tp) cc_final: 0.7827 (tp) REVERT: A 609 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 615 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7223 (tp30) REVERT: B 270 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7760 (mtm-85) REVERT: B 445 TYR cc_start: 0.8237 (m-80) cc_final: 0.7883 (m-80) REVERT: B 468 ARG cc_start: 0.7357 (ttp80) cc_final: 0.6298 (ttm170) REVERT: B 508 MET cc_start: 0.7881 (tpt) cc_final: 0.7672 (tpp) REVERT: B 550 GLU cc_start: 0.8248 (pm20) cc_final: 0.7886 (pm20) REVERT: B 565 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 579 ILE cc_start: 0.8053 (tp) cc_final: 0.7800 (tp) REVERT: B 609 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6896 (t80) REVERT: B 615 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7471 (tp30) outliers start: 23 outliers final: 17 residues processed: 97 average time/residue: 0.0693 time to fit residues: 9.2546 Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 72.7434 > 50: distance: 20 - 26: 28.573 distance: 26 - 27: 13.100 distance: 28 - 29: 56.647 distance: 28 - 36: 69.014 distance: 29 - 59: 37.981 distance: 31 - 32: 57.268 distance: 31 - 33: 57.246 distance: 32 - 34: 38.726 distance: 33 - 35: 58.380 distance: 34 - 35: 45.541 distance: 36 - 37: 39.460 distance: 37 - 38: 56.479 distance: 38 - 39: 39.585 distance: 38 - 43: 41.149 distance: 40 - 41: 55.616 distance: 40 - 42: 41.128 distance: 43 - 44: 40.585 distance: 44 - 45: 13.338 distance: 44 - 47: 38.693 distance: 45 - 46: 41.268 distance: 45 - 51: 27.220 distance: 47 - 48: 55.540 distance: 48 - 50: 56.682 distance: 51 - 52: 40.947 distance: 52 - 53: 55.819 distance: 53 - 54: 57.566 distance: 53 - 59: 40.362 distance: 55 - 56: 64.229 distance: 55 - 57: 67.922 distance: 56 - 58: 41.180 distance: 59 - 60: 40.359 distance: 60 - 61: 56.567 distance: 60 - 63: 7.120 distance: 61 - 62: 57.157 distance: 61 - 70: 39.056 distance: 63 - 64: 8.326 distance: 64 - 65: 55.736 distance: 65 - 67: 39.782 distance: 66 - 68: 55.665 distance: 68 - 69: 38.632 distance: 70 - 71: 40.336 distance: 71 - 72: 39.892 distance: 72 - 79: 40.400 distance: 74 - 75: 55.788 distance: 75 - 76: 38.921 distance: 76 - 78: 55.609 distance: 79 - 80: 57.761 distance: 80 - 81: 40.178 distance: 80 - 83: 57.088 distance: 81 - 87: 55.638 distance: 83 - 84: 56.141 distance: 84 - 85: 40.677 distance: 84 - 86: 40.303 distance: 88 - 89: 68.011 distance: 88 - 91: 57.394 distance: 89 - 90: 39.817 distance: 89 - 95: 57.534 distance: 91 - 92: 40.713 distance: 92 - 93: 56.775 distance: 92 - 94: 39.672 distance: 95 - 96: 55.227 distance: 95 - 101: 57.042 distance: 96 - 97: 39.666 distance: 96 - 99: 68.974 distance: 97 - 102: 40.951 distance: 99 - 100: 7.935 distance: 100 - 101: 65.917 distance: 102 - 103: 69.555 distance: 103 - 104: 56.743 distance: 103 - 106: 40.826 distance: 104 - 105: 38.892 distance: 104 - 113: 34.205 distance: 106 - 107: 57.047 distance: 107 - 108: 39.251 distance: 108 - 109: 40.018 distance: 109 - 110: 55.378 distance: 110 - 111: 69.580 distance: 110 - 112: 40.579