Starting phenix.real_space_refine on Tue Feb 3 20:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3f_72192/02_2026/9q3f_72192.map" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 39 5.16 5 C 4195 2.51 5 N 1186 2.21 5 O 1187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 6615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6438 Classifications: {'peptide': 801} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 7} Link IDs: {'rna2p': 1, 'rna3p': 6} Time building chain proxies: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6615 At special positions: 0 Unit cell: (75.264, 93.184, 107.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 8 15.00 O 1187 8.00 N 1186 7.00 C 4195 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: 0.51 Conformation dependent library (CDL) restraints added in 153.4 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 35.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.896A pdb=" N ILE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 368 through 384 removed outlier: 4.059A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 461 through 478 removed outlier: 3.875A pdb=" N LYS A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.855A pdb=" N VAL A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.928A pdb=" N PHE A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 585 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 586 " --> pdb=" O VAL A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 586' Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 672 through 692 removed outlier: 3.887A pdb=" N ILE A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 692 " --> pdb=" O CYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.570A pdb=" N VAL A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 844 removed outlier: 4.387A pdb=" N ALA A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 405 removed outlier: 3.728A pdb=" N VAL A 405 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 202 removed outlier: 3.715A pdb=" N SER A 217 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 210 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 397 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 4.402A pdb=" N ASN A 280 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 326 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 490 removed outlier: 7.297A pdb=" N ILE A 450 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 622 through 624 removed outlier: 4.010A pdb=" N SER A 607 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 622 through 624 removed outlier: 5.757A pdb=" N PHE A 590 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 664 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 666 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 595 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A 766 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 703 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL A 764 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN A 705 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR A 762 " --> pdb=" O GLN A 705 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 705 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: 0.99 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2020 1.34 - 1.45: 980 1.45 - 1.57: 3720 1.57 - 1.69: 15 1.69 - 1.81: 58 Bond restraints: 6793 Sorted by residual: bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.494 -0.030 1.02e-02 9.61e+03 8.37e+00 bond pdb=" N ILE A 150 " pdb=" CA ILE A 150 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.15e+00 bond pdb=" N GLU A 680 " pdb=" CA GLU A 680 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.35e+00 bond pdb=" N TYR A 679 " pdb=" CA TYR A 679 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.91e+00 bond pdb=" N GLN A 149 " pdb=" CA GLN A 149 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.54e+00 ... (remaining 6788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 8936 1.30 - 2.60: 250 2.60 - 3.89: 46 3.89 - 5.19: 6 5.19 - 6.49: 4 Bond angle restraints: 9242 Sorted by residual: angle pdb=" CA GLU A 680 " pdb=" C GLU A 680 " pdb=" O GLU A 680 " ideal model delta sigma weight residual 120.82 117.76 3.06 1.05e+00 9.07e-01 8.47e+00 angle pdb=" CA PRO A 151 " pdb=" C PRO A 151 " pdb=" O PRO A 151 " ideal model delta sigma weight residual 121.95 118.52 3.43 1.25e+00 6.40e-01 7.53e+00 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 angle pdb=" N LEU A 681 " pdb=" CA LEU A 681 " pdb=" C LEU A 681 " ideal model delta sigma weight residual 111.28 108.53 2.75 1.09e+00 8.42e-01 6.34e+00 angle pdb=" CA TYR A 679 " pdb=" C TYR A 679 " pdb=" O TYR A 679 " ideal model delta sigma weight residual 121.07 118.38 2.69 1.10e+00 8.26e-01 5.96e+00 ... (remaining 9237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3670 17.15 - 34.31: 367 34.31 - 51.46: 54 51.46 - 68.61: 14 68.61 - 85.77: 7 Dihedral angle restraints: 4112 sinusoidal: 1767 harmonic: 2345 Sorted by residual: dihedral pdb=" CA LEU A 133 " pdb=" C LEU A 133 " pdb=" N ALA A 134 " pdb=" CA ALA A 134 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU A 670 " pdb=" CG GLU A 670 " pdb=" CD GLU A 670 " pdb=" OE1 GLU A 670 " ideal model delta sinusoidal sigma weight residual 0.00 -85.56 85.56 1 3.00e+01 1.11e-03 9.84e+00 dihedral pdb=" CA CYS A 452 " pdb=" C CYS A 452 " pdb=" N PHE A 453 " pdb=" CA PHE A 453 " ideal model delta harmonic sigma weight residual 180.00 -164.43 -15.57 0 5.00e+00 4.00e-02 9.70e+00 ... (remaining 4109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 704 0.037 - 0.074: 198 0.074 - 0.111: 88 0.111 - 0.148: 26 0.148 - 0.184: 2 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE A 237 " pdb=" CA ILE A 237 " pdb=" CG1 ILE A 237 " pdb=" CG2 ILE A 237 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA VAL A 152 " pdb=" N VAL A 152 " pdb=" C VAL A 152 " pdb=" CB VAL A 152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1015 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 225 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO A 226 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 796 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 797 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 797 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 797 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 181 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 182 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.024 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 408 2.74 - 3.28: 6026 3.28 - 3.82: 9646 3.82 - 4.36: 10735 4.36 - 4.90: 19449 Nonbonded interactions: 46264 Sorted by model distance: nonbonded pdb=" OD1 ASP A 58 " pdb=" OG SER A 129 " model vdw 2.196 3.040 nonbonded pdb=" O TYR A 42 " pdb=" OG1 THR A 403 " model vdw 2.250 3.040 nonbonded pdb=" ND1 HIS A 739 " pdb=" OE1 GLU A 742 " model vdw 2.269 3.120 nonbonded pdb=" O VAL A 175 " pdb=" OG SER A 178 " model vdw 2.299 3.040 nonbonded pdb=" NE2 HIS A 597 " pdb=" OE2 GLU A 634 " model vdw 2.310 3.120 ... (remaining 46259 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: 7.550 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: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.610 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.033 6793 Z= 0.143 Angle : 0.527 6.490 9242 Z= 0.287 Chirality : 0.044 0.184 1018 Planarity : 0.004 0.063 1163 Dihedral : 13.850 85.765 2600 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.28 % Allowed : 0.43 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.50 (0.31), residues: 793 helix: 1.51 (0.34), residues: 257 sheet: -0.63 (0.43), residues: 159 loop : -1.53 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.021 0.001 TYR A 801 PHE 0.010 0.001 PHE A 741 TRP 0.005 0.001 TRP A 432 HIS 0.004 0.001 HIS A 761 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6793) covalent geometry : angle 0.52660 ( 9242) hydrogen bonds : bond 0.20015 ( 247) hydrogen bonds : angle 6.62278 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.250 Fit side-chains REVERT: A 29 ILE cc_start: 0.7942 (mm) cc_final: 0.7720 (mm) REVERT: A 71 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7412 (mt-10) REVERT: A 258 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 263 LYS cc_start: 0.6966 (mmtp) cc_final: 0.6472 (mmtm) REVERT: A 450 ILE cc_start: 0.8402 (mt) cc_final: 0.8134 (tt) REVERT: A 634 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 686 ASP cc_start: 0.8439 (t70) cc_final: 0.8022 (t0) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.0849 time to fit residues: 14.4118 Evaluate side-chains 78 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 386 ASN A 579 GLN A 761 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116836 restraints weight = 8469.315| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.99 r_work: 0.3123 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6793 Z= 0.161 Angle : 0.608 6.534 9242 Z= 0.319 Chirality : 0.046 0.157 1018 Planarity : 0.006 0.063 1163 Dihedral : 6.332 88.271 981 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.70 % Allowed : 8.79 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.31), residues: 793 helix: 1.41 (0.34), residues: 258 sheet: -0.40 (0.42), residues: 158 loop : -1.64 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 25 TYR 0.019 0.002 TYR A 701 PHE 0.013 0.001 PHE A 743 TRP 0.004 0.001 TRP A 448 HIS 0.004 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6793) covalent geometry : angle 0.60787 ( 9242) hydrogen bonds : bond 0.05668 ( 247) hydrogen bonds : angle 5.01981 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7501 (mt-10) REVERT: A 185 TYR cc_start: 0.6983 (m-10) cc_final: 0.6465 (m-80) REVERT: A 258 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 272 MET cc_start: 0.6452 (tmm) cc_final: 0.6230 (tmm) REVERT: A 496 ASP cc_start: 0.8014 (t0) cc_final: 0.7645 (t0) REVERT: A 686 ASP cc_start: 0.8356 (t70) cc_final: 0.7886 (t0) REVERT: A 742 GLU cc_start: 0.7332 (mp0) cc_final: 0.7119 (mp0) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.0832 time to fit residues: 10.8496 Evaluate side-chains 88 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 801 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 79 HIS A 201 GLN ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.163808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117132 restraints weight = 8425.291| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.32 r_work: 0.3134 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6793 Z= 0.185 Angle : 0.590 6.344 9242 Z= 0.311 Chirality : 0.046 0.159 1018 Planarity : 0.005 0.063 1163 Dihedral : 6.338 86.334 981 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.27 % Allowed : 12.48 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.44 (0.31), residues: 793 helix: 1.47 (0.34), residues: 258 sheet: -0.31 (0.43), residues: 155 loop : -1.58 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.012 0.002 TYR A 812 PHE 0.011 0.001 PHE A 199 TRP 0.007 0.001 TRP A 448 HIS 0.006 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 6793) covalent geometry : angle 0.59016 ( 9242) hydrogen bonds : bond 0.06526 ( 247) hydrogen bonds : angle 5.10093 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.251 Fit side-chains REVERT: A 71 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7553 (mt-10) REVERT: A 185 TYR cc_start: 0.7245 (m-10) cc_final: 0.6791 (m-80) REVERT: A 258 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8001 (mm-30) REVERT: A 263 LYS cc_start: 0.7439 (mttm) cc_final: 0.6893 (mmtm) REVERT: A 272 MET cc_start: 0.6586 (tmm) cc_final: 0.6324 (tmm) REVERT: A 496 ASP cc_start: 0.8165 (t0) cc_final: 0.7843 (t0) REVERT: A 686 ASP cc_start: 0.8380 (t70) cc_final: 0.7956 (t0) REVERT: A 734 ASP cc_start: 0.7762 (t0) cc_final: 0.7433 (t0) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 0.0801 time to fit residues: 10.5626 Evaluate side-chains 89 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 801 TYR 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: 50.2081 > 50: distance: 51 - 55: 3.747 distance: 55 - 56: 3.819 distance: 56 - 57: 4.571 distance: 56 - 59: 3.519 distance: 57 - 58: 3.766 distance: 62 - 64: 3.675 distance: 67 - 70: 5.142 distance: 70 - 71: 6.363 distance: 73 - 74: 3.408 distance: 81 - 82: 3.203 distance: 82 - 83: 3.846 distance: 83 - 84: 4.581 distance: 83 - 93: 4.012 distance: 93 - 94: 3.106 distance: 94 - 95: 13.044 distance: 94 - 97: 6.574 distance: 95 - 96: 15.228 distance: 95 - 98: 6.932 distance: 98 - 99: 4.110 distance: 99 - 100: 18.857 distance: 99 - 102: 13.424 distance: 100 - 101: 26.159 distance: 100 - 107: 19.664 distance: 102 - 103: 7.496 distance: 103 - 104: 9.435 distance: 104 - 105: 5.964 distance: 104 - 106: 4.347 distance: 107 - 108: 21.947 distance: 108 - 109: 19.633 distance: 109 - 110: 27.271 distance: 109 - 111: 21.310 distance: 111 - 112: 10.348 distance: 112 - 115: 13.773 distance: 113 - 114: 8.324 distance: 113 - 116: 9.514 distance: 116 - 117: 6.155 distance: 117 - 120: 6.194 distance: 118 - 119: 4.030 distance: 118 - 124: 4.164 distance: 120 - 121: 3.100 distance: 121 - 123: 4.988 distance: 125 - 126: 3.642 distance: 126 - 127: 4.589 distance: 128 - 129: 7.138