Starting phenix.real_space_refine on Fri Aug 22 12:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2025/8spa_40677.map" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.002 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 5 5.16 5 C 1210 2.51 5 N 300 2.21 5 O 355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 374 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.36, per 1000 atoms: 0.19 Number of scatterers: 1870 At special positions: 0 Unit cell: (63.64, 61.06, 48.16, 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 5 16.00 O 355 8.00 N 300 7.00 C 1210 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: 0.08 Conformation dependent library (CDL) restraints added in 45.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 430 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 37 removed outlier: 6.782A pdb=" N MET A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLN C 36 " --> pdb=" O MET A 33 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN E 36 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.11 Time building geometry restraints manager: 0.11 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: 585 1.34 - 1.46: 441 1.46 - 1.57: 904 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 1940 Sorted by residual: bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 1935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2416 1.10 - 2.19: 169 2.19 - 3.29: 54 3.29 - 4.39: 6 4.39 - 5.48: 10 Bond angle restraints: 2655 Sorted by residual: angle pdb=" C PRO D 39 " pdb=" N HIS D 40 " pdb=" CA HIS D 40 " ideal model delta sigma weight residual 122.08 118.87 3.21 1.59e+00 3.96e-01 4.06e+00 angle pdb=" C PRO B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.01e+00 angle pdb=" C PRO E 39 " pdb=" N HIS E 40 " pdb=" CA HIS E 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" C PRO A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta sigma weight residual 122.08 118.94 3.14 1.59e+00 3.96e-01 3.89e+00 angle pdb=" C PRO C 39 " pdb=" N HIS C 40 " pdb=" CA HIS C 40 " ideal model delta sigma weight residual 122.08 118.97 3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 2650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.72: 796 6.72 - 13.44: 129 13.44 - 20.17: 75 20.17 - 26.89: 30 26.89 - 33.61: 20 Dihedral angle restraints: 1050 sinusoidal: 380 harmonic: 670 Sorted by residual: dihedral pdb=" CA HIS A 40 " pdb=" C HIS A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA HIS B 40 " pdb=" C HIS B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA HIS D 40 " pdb=" C HIS D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 151 0.030 - 0.060: 94 0.060 - 0.090: 23 0.090 - 0.120: 7 0.120 - 0.150: 10 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA HIS C 40 " pdb=" N HIS C 40 " pdb=" C HIS C 40 " pdb=" CB HIS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA HIS B 40 " pdb=" N HIS B 40 " pdb=" C HIS B 40 " pdb=" CB HIS B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA HIS E 40 " pdb=" N HIS E 40 " pdb=" C HIS E 40 " pdb=" CB HIS E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 282 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 43 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.019 5.00e-02 4.00e+02 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1221 3.07 - 3.53: 1837 3.53 - 3.99: 2653 3.99 - 4.44: 3041 4.44 - 4.90: 5102 Nonbonded interactions: 13854 Sorted by model distance: nonbonded pdb=" O HIS D 40 " pdb=" ND1 HIS D 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS B 40 " pdb=" ND1 HIS B 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS E 40 " pdb=" ND1 HIS E 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS A 40 " pdb=" ND1 HIS A 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS C 40 " pdb=" ND1 HIS C 41 " model vdw 2.614 3.120 ... (remaining 13849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.260 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:4.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.038 1940 Z= 0.239 Angle : 0.753 5.482 2655 Z= 0.403 Chirality : 0.045 0.150 285 Planarity : 0.005 0.034 350 Dihedral : 10.816 33.609 620 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.42), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 38 TRP 0.001 0.001 TRP D 10 HIS 0.005 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 1940) covalent geometry : angle 0.75278 ( 2655) hydrogen bonds : bond 0.21596 ( 10) hydrogen bonds : angle 7.11050 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.041 Fit side-chains REVERT: C 10 TRP cc_start: 0.7650 (t-100) cc_final: 0.6809 (t-100) REVERT: D 19 GLU cc_start: 0.7977 (tt0) cc_final: 0.7568 (tm-30) REVERT: E 33 MET cc_start: 0.8984 (mtp) cc_final: 0.8663 (mtt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.3194 time to fit residues: 14.4403 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.095657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080783 restraints weight = 4619.126| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.66 r_work: 0.3764 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1940 Z= 0.157 Angle : 0.687 5.117 2655 Z= 0.348 Chirality : 0.043 0.147 285 Planarity : 0.003 0.018 350 Dihedral : 6.325 20.491 240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE B 38 TRP 0.007 0.001 TRP E 10 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 1940) covalent geometry : angle 0.68688 ( 2655) hydrogen bonds : bond 0.03754 ( 10) hydrogen bonds : angle 5.59144 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7858 (t-100) cc_final: 0.7070 (t-100) REVERT: E 33 MET cc_start: 0.9076 (mtp) cc_final: 0.8861 (mtt) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.2153 time to fit residues: 7.7848 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.091824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.076290 restraints weight = 4677.633| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.78 r_work: 0.3727 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.132 Angle : 0.651 5.620 2655 Z= 0.323 Chirality : 0.041 0.143 285 Planarity : 0.003 0.018 350 Dihedral : 5.985 20.120 240 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.86 % Allowed : 17.62 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 35 TRP 0.006 0.001 TRP E 10 HIS 0.005 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1940) covalent geometry : angle 0.65076 ( 2655) hydrogen bonds : bond 0.02623 ( 10) hydrogen bonds : angle 5.13032 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7948 (t-100) cc_final: 0.6673 (t-100) REVERT: E 10 TRP cc_start: 0.7322 (t-100) cc_final: 0.5516 (p-90) REVERT: E 33 MET cc_start: 0.9152 (mtp) cc_final: 0.8148 (pmt) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.1692 time to fit residues: 5.2913 Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.176504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.145329 restraints weight = 4700.078| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.21 r_work: 0.3713 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1940 Z= 0.130 Angle : 0.666 7.862 2655 Z= 0.318 Chirality : 0.041 0.140 285 Planarity : 0.003 0.023 350 Dihedral : 5.870 20.434 240 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.38 % Allowed : 20.95 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 35 TRP 0.006 0.001 TRP E 10 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1940) covalent geometry : angle 0.66639 ( 2655) hydrogen bonds : bond 0.02302 ( 10) hydrogen bonds : angle 4.59088 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7961 (t-100) cc_final: 0.6758 (t-100) REVERT: E 10 TRP cc_start: 0.7334 (t-100) cc_final: 0.5428 (p-90) REVERT: E 33 MET cc_start: 0.9154 (mtp) cc_final: 0.8147 (pmt) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.3413 time to fit residues: 9.5368 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.7906 > 50: distance: 111 - 119: 9.792 distance: 119 - 120: 5.596 distance: 120 - 121: 4.631 distance: 120 - 123: 9.977 distance: 121 - 125: 25.878 distance: 123 - 124: 20.761 distance: 125 - 126: 14.067 distance: 126 - 127: 23.867 distance: 126 - 129: 8.741 distance: 127 - 128: 32.497 distance: 127 - 132: 26.883 distance: 129 - 130: 9.899 distance: 129 - 131: 19.430 distance: 132 - 133: 11.064 distance: 133 - 134: 23.797 distance: 134 - 135: 21.830 distance: 134 - 136: 27.715 distance: 136 - 137: 19.164 distance: 137 - 138: 16.654 distance: 137 - 140: 3.164 distance: 138 - 139: 23.433 distance: 138 - 143: 19.598 distance: 140 - 141: 17.205 distance: 140 - 142: 29.942 distance: 143 - 144: 12.592 distance: 144 - 145: 9.306 distance: 144 - 147: 5.652 distance: 145 - 146: 31.822 distance: 145 - 150: 7.834 distance: 147 - 148: 10.258 distance: 147 - 149: 24.136 distance: 150 - 151: 12.444 distance: 151 - 152: 13.286 distance: 151 - 154: 12.845 distance: 152 - 153: 14.724 distance: 152 - 158: 36.931 distance: 154 - 155: 6.638 distance: 155 - 156: 7.312 distance: 155 - 157: 12.453 distance: 158 - 159: 5.725 distance: 159 - 160: 18.901 distance: 159 - 162: 7.080 distance: 160 - 161: 24.082 distance: 160 - 163: 29.135 distance: 163 - 164: 26.235 distance: 164 - 165: 33.457 distance: 164 - 167: 24.809 distance: 165 - 166: 11.188 distance: 165 - 170: 13.297 distance: 167 - 168: 30.345 distance: 167 - 169: 37.711 distance: 170 - 171: 28.550 distance: 171 - 172: 27.772 distance: 171 - 174: 13.454 distance: 172 - 173: 6.591 distance: 172 - 179: 12.960 distance: 174 - 175: 20.649 distance: 175 - 176: 18.768 distance: 176 - 177: 24.766 distance: 176 - 178: 21.332 distance: 179 - 180: 22.466 distance: 180 - 181: 7.195 distance: 180 - 183: 13.007 distance: 181 - 182: 5.945 distance: 181 - 187: 25.890 distance: 183 - 184: 35.843 distance: 184 - 185: 21.793 distance: 184 - 186: 32.785