Starting phenix.real_space_refine on Sat May 2 15:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9g_64871/05_2026/9v9g_64871.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 34 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 4148 2.51 5 N 1228 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6052 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 42, 'TRANS': 717} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 1, 'rna3p': 14} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'water': 16} Link IDs: {None: 18} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.27 Number of scatterers: 6784 At special positions: 0 Unit cell: (74.888, 88.504, 102.12, 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 15 16.00 P 34 15.00 Mg 3 11.99 O 1356 8.00 N 1228 7.00 C 4148 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: 0.63 Conformation dependent library (CDL) restraints added in 472.9 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 33.0% alpha, 23.0% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.027A pdb=" N ALA A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 392 removed outlier: 4.619A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 621 through 638 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 749 through 762 removed outlier: 4.366A pdb=" N SER A 755 " --> pdb=" O THR A 751 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 5.536A pdb=" N ARG A 137 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE A 144 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.729A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU A 99 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ARG A 27 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 97 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 232 through 239 removed outlier: 3.756A pdb=" N GLY A 234 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 removed outlier: 7.282A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 575 removed outlier: 6.137A pdb=" N LEU A 551 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1841 1.33 - 1.45: 1331 1.45 - 1.57: 3717 1.57 - 1.69: 66 1.69 - 1.81: 23 Bond restraints: 6978 Sorted by residual: bond pdb=" N PHE A 205 " pdb=" CA PHE A 205 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.40e-02 5.10e+03 4.60e+00 bond pdb=" N HIS A 204 " pdb=" CA HIS A 204 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.20e-02 6.94e+03 4.47e+00 bond pdb=" CG HIS A 204 " pdb=" CD2 HIS A 204 " ideal model delta sigma weight residual 1.354 1.335 0.019 1.10e-02 8.26e+03 2.84e+00 bond pdb=" CA GLY A 172 " pdb=" C GLY A 172 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.82e+00 bond pdb=" C GLU A 64 " pdb=" N TRP A 65 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.07e-02 2.33e+03 2.35e+00 ... (remaining 6973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.09: 9618 5.09 - 10.18: 5 10.18 - 15.27: 0 15.27 - 20.37: 0 20.37 - 25.46: 1 Bond angle restraints: 9624 Sorted by residual: angle pdb=" C LEU A 577 " pdb=" CA LEU A 577 " pdb=" CB LEU A 577 " ideal model delta sigma weight residual 115.89 110.29 5.60 1.32e+00 5.74e-01 1.80e+01 angle pdb=" C GLN A 260 " pdb=" N ARG A 261 " pdb=" CA ARG A 261 " ideal model delta sigma weight residual 122.56 115.28 7.28 1.72e+00 3.38e-01 1.79e+01 angle pdb=" C GLU A 64 " pdb=" N TRP A 65 " pdb=" CA TRP A 65 " ideal model delta sigma weight residual 120.30 145.76 -25.46 6.38e+00 2.46e-02 1.59e+01 angle pdb=" CA TYR A 257 " pdb=" CB TYR A 257 " pdb=" CG TYR A 257 " ideal model delta sigma weight residual 113.90 120.38 -6.48 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C LEU A 203 " pdb=" N HIS A 204 " pdb=" CA HIS A 204 " ideal model delta sigma weight residual 120.44 115.95 4.49 1.36e+00 5.41e-01 1.09e+01 ... (remaining 9619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 3929 26.91 - 53.81: 196 53.81 - 80.72: 33 80.72 - 107.62: 0 107.62 - 134.53: 1 Dihedral angle restraints: 4159 sinusoidal: 1967 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 85.47 134.53 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA TYR A 543 " pdb=" C TYR A 543 " pdb=" N ASP A 544 " pdb=" CA ASP A 544 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLY A 224 " pdb=" C GLY A 224 " pdb=" N LYS A 225 " pdb=" CA LYS A 225 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 4156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 726 0.031 - 0.062: 237 0.062 - 0.093: 58 0.093 - 0.124: 46 0.124 - 0.156: 9 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA ASP A 329 " pdb=" N ASP A 329 " pdb=" C ASP A 329 " pdb=" CB ASP A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE A 689 " pdb=" N ILE A 689 " pdb=" C ILE A 689 " pdb=" CB ILE A 689 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ARG A 261 " pdb=" N ARG A 261 " pdb=" C ARG A 261 " pdb=" CB ARG A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1073 not shown) Planarity restraints: 1141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 470 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 471 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 471 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 471 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 257 " -0.020 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR A 257 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 257 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 257 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 257 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 257 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 533 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 534 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.023 5.00e-02 4.00e+02 ... (remaining 1138 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 559 2.74 - 3.28: 5977 3.28 - 3.82: 10839 3.82 - 4.36: 13865 4.36 - 4.90: 23046 Nonbonded interactions: 54286 Sorted by model distance: nonbonded pdb=" OG SER A 125 " pdb=" O TRP A 140 " model vdw 2.204 3.040 nonbonded pdb=" OP1 U C 7 " pdb="MG MG A 803 " model vdw 2.260 2.170 nonbonded pdb=" O PRO A 309 " pdb=" O HOH A 901 " model vdw 2.285 3.040 nonbonded pdb=" NE2 GLN A 576 " pdb=" O LYS A 585 " model vdw 2.286 3.120 nonbonded pdb=" OD1 ASP A 544 " pdb=" O HOH A 902 " model vdw 2.298 3.040 ... (remaining 54281 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.010 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: 0.000 Load rotamer database and sin/cos tables:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.003 0.048 6978 Z= 0.144 Angle : 0.578 25.457 9624 Z= 0.290 Chirality : 0.040 0.156 1076 Planarity : 0.005 0.052 1141 Dihedral : 15.492 134.526 2747 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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 are not related in a simple way. whole: 0.69 (0.31), residues: 758 helix: 1.57 (0.35), residues: 221 sheet: 0.75 (0.40), residues: 185 loop : -0.37 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 261 TYR 0.031 0.002 TYR A 257 PHE 0.012 0.001 PHE A 545 TRP 0.014 0.001 TRP A 620 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6978) covalent geometry : angle 0.57797 ( 9624) hydrogen bonds : bond 0.15133 ( 304) hydrogen bonds : angle 6.42736 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.256 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.6863 time to fit residues: 46.7129 Evaluate side-chains 42 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 684 ASN A 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121308 restraints weight = 7631.087| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.14 r_work: 0.3104 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6978 Z= 0.145 Angle : 0.563 19.386 9624 Z= 0.289 Chirality : 0.041 0.162 1076 Planarity : 0.005 0.045 1141 Dihedral : 15.277 135.639 1271 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.62 % Allowed : 7.42 % Favored : 91.96 % 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: 0.85 (0.31), residues: 758 helix: 1.80 (0.35), residues: 231 sheet: 0.92 (0.40), residues: 179 loop : -0.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 261 TYR 0.025 0.002 TYR A 257 PHE 0.011 0.001 PHE A 545 TRP 0.012 0.001 TRP A 136 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6978) covalent geometry : angle 0.56298 ( 9624) hydrogen bonds : bond 0.04777 ( 304) hydrogen bonds : angle 4.99318 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 208 SER cc_start: 0.7835 (m) cc_final: 0.7194 (m) REVERT: A 218 MET cc_start: 0.9040 (mtp) cc_final: 0.8795 (mtm) outliers start: 4 outliers final: 0 residues processed: 49 average time/residue: 0.5374 time to fit residues: 28.0660 Evaluate side-chains 43 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5043 > 50: distance: 10 - 183: 20.831 distance: 13 - 180: 7.237 distance: 22 - 164: 9.960 distance: 25 - 161: 10.623 distance: 79 - 175: 7.154 distance: 82 - 172: 3.792 distance: 93 - 159: 22.863 distance: 102 - 104: 9.682 distance: 104 - 105: 22.552 distance: 105 - 106: 31.218 distance: 105 - 108: 14.926 distance: 106 - 107: 27.086 distance: 106 - 115: 35.972 distance: 108 - 109: 6.054 distance: 109 - 110: 3.882 distance: 115 - 116: 5.395 distance: 116 - 117: 16.226 distance: 116 - 119: 11.666 distance: 117 - 118: 11.396 distance: 117 - 126: 7.492 distance: 119 - 120: 10.446 distance: 120 - 121: 8.577 distance: 120 - 122: 6.988 distance: 121 - 123: 7.113 distance: 122 - 124: 7.338 distance: 124 - 125: 3.834 distance: 126 - 127: 23.073 distance: 127 - 128: 38.280 distance: 127 - 130: 19.109 distance: 128 - 129: 34.027 distance: 128 - 135: 33.064 distance: 130 - 131: 12.461 distance: 131 - 132: 7.439 distance: 132 - 133: 6.488 distance: 132 - 134: 5.113 distance: 135 - 136: 34.217 distance: 136 - 137: 44.179 distance: 136 - 139: 28.829 distance: 137 - 138: 49.385 distance: 137 - 149: 30.713 distance: 139 - 140: 18.220 distance: 140 - 141: 8.065 distance: 140 - 142: 3.685 distance: 141 - 143: 4.754 distance: 142 - 145: 8.062 distance: 143 - 144: 4.048 distance: 145 - 147: 9.513 distance: 146 - 148: 5.841 distance: 147 - 148: 8.147 distance: 149 - 150: 23.031 distance: 149 - 155: 33.004 distance: 150 - 151: 29.389 distance: 150 - 153: 29.416 distance: 151 - 152: 14.972 distance: 151 - 156: 21.372 distance: 153 - 154: 4.750 distance: 154 - 155: 23.647 distance: 156 - 157: 14.832 distance: 157 - 158: 20.247 distance: 157 - 160: 18.493 distance: 158 - 159: 18.662 distance: 158 - 161: 23.342 distance: 161 - 162: 16.734 distance: 162 - 163: 7.310 distance: 162 - 165: 6.249 distance: 163 - 164: 7.876 distance: 163 - 172: 9.477 distance: 165 - 166: 3.391 distance: 166 - 168: 5.950 distance: 168 - 170: 4.176 distance: 172 - 173: 4.419 distance: 173 - 174: 8.283 distance: 173 - 176: 5.289 distance: 174 - 180: 4.961 distance: 176 - 177: 6.803 distance: 177 - 179: 5.155 distance: 180 - 181: 7.985 distance: 181 - 182: 14.615 distance: 181 - 184: 26.744 distance: 182 - 183: 9.141 distance: 182 - 187: 11.818 distance: 184 - 185: 15.979 distance: 184 - 186: 18.648 distance: 187 - 188: 15.098 distance: 187 - 193: 27.814 distance: 188 - 189: 11.386 distance: 188 - 191: 6.643 distance: 189 - 190: 31.678 distance: 189 - 194: 7.363 distance: 191 - 192: 16.667 distance: 192 - 193: 9.829