Starting phenix.real_space_refine on Wed Jul 1 21:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.map" model { file = "/net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knw_62464/07_2026/9knw_62464.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.86, per 1000 atoms: 0.31 Number of scatterers: 2747 At special positions: 0 Unit cell: (81.51, 93.48, 86.07, 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 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.25 Conformation dependent library (CDL) restraints added in 77.4 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 60.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.789A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.688A pdb=" N HIS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.988A pdb=" N MET A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.055A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 46 No H-bonds generated for 'chain 'A' and resid 45 through 46' Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.647A pdb=" N ILE A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.695A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.104A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 465 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: 0.32 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 778 1.43 - 1.55: 1578 1.55 - 1.68: 20 1.68 - 1.81: 29 Bond restraints: 2814 Sorted by residual: bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.331 1.430 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.339 1.436 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C60 CDL B 201 " pdb=" C61 CDL B 201 " ideal model delta sigma weight residual 1.527 1.605 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 3726 3.13 - 6.25: 47 6.25 - 9.38: 5 9.38 - 12.51: 6 12.51 - 15.63: 3 Bond angle restraints: 3787 Sorted by residual: angle pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sigma weight residual 93.28 108.91 -15.63 3.00e+00 1.11e-01 2.72e+01 angle pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB5 CDL B 201 " ideal model delta sigma weight residual 96.70 109.87 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" OA3 CDL B 201 " pdb=" PA1 CDL B 201 " pdb=" OA4 CDL B 201 " ideal model delta sigma weight residual 121.92 109.38 12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" OB3 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB4 CDL B 201 " ideal model delta sigma weight residual 121.80 109.47 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CB GLU B 21 " pdb=" CG GLU B 21 " pdb=" CD GLU B 21 " ideal model delta sigma weight residual 112.60 106.09 6.51 1.70e+00 3.46e-01 1.47e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 1570 29.66 - 59.32: 134 59.32 - 88.98: 4 88.98 - 118.64: 0 118.64 - 148.30: 1 Dihedral angle restraints: 1709 sinusoidal: 750 harmonic: 959 Sorted by residual: dihedral pdb=" C1 PC8 A 201 " pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sinusoidal sigma weight residual 166.83 -44.87 -148.30 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.46 32.46 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLU A 49 " pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " ideal model delta sinusoidal sigma weight residual 60.00 118.30 -58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 281 0.042 - 0.083: 84 0.083 - 0.124: 20 0.124 - 0.165: 6 0.165 - 0.207: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C7 PC8 A 201 " pdb=" C6 PC8 A 201 " pdb=" C8 PC8 A 201 " pdb=" O7 PC8 A 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PHE A 66 " pdb=" N PHE A 66 " pdb=" C PHE A 66 " pdb=" CB PHE A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU B 21 " pdb=" N GLU B 21 " pdb=" C GLU B 21 " pdb=" CB GLU B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 34 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 35 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 66 " -0.015 2.00e-02 2.50e+03 1.31e-02 3.00e+00 pdb=" CG PHE A 66 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 66 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 29 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 30 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 852 2.82 - 3.34: 2563 3.34 - 3.86: 4571 3.86 - 4.38: 5225 4.38 - 4.90: 8698 Nonbonded interactions: 21909 Sorted by model distance: nonbonded pdb=" NH1 ARG C 38 " pdb=" OD1 ASP C 90 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN C 13 " pdb=" O SER C 114 " model vdw 2.326 3.120 nonbonded pdb=" NE1 TRP B 82 " pdb=" O GLY A 29 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP C 52 " pdb=" N SER C 57 " model vdw 2.339 3.120 nonbonded pdb=" N ASP A 17 " pdb=" OD1 ASP A 17 " model vdw 2.354 3.120 ... (remaining 21904 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: 1.680 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: 0.090 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.500 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.008 0.107 2815 Z= 0.387 Angle : 1.023 15.635 3789 Z= 0.477 Chirality : 0.044 0.207 392 Planarity : 0.005 0.045 464 Dihedral : 19.145 148.303 1092 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.35 (0.42), residues: 327 helix: -0.39 (0.35), residues: 169 sheet: -1.23 (0.64), residues: 57 loop : -1.25 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.018 0.002 TYR C 95 PHE 0.027 0.002 PHE A 66 TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.39 ( 2814) covalent geometry : angle 1.02327 / 0.48 ( 3787) SS BOND : bond 0.00508 / 0.27 ( 1) SS BOND : angle 1.10010 / 0.64 ( 2) hydrogen bonds : bond 0.11730 / 7.65 ( 166) hydrogen bonds : angle 5.43762 / 4.03 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7771 (tt0) REVERT: A 18 PHE cc_start: 0.6364 (t80) cc_final: 0.6059 (p90) outliers start: 4 outliers final: 4 residues processed: 87 average time/residue: 0.0571 time to fit residues: 5.7076 Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 HIS ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.191395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155884 restraints weight = 3890.938| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.88 r_work: 0.3720 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.138 Angle : 0.569 8.042 3789 Z= 0.290 Chirality : 0.040 0.133 392 Planarity : 0.005 0.053 464 Dihedral : 16.500 114.101 499 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.33 % Allowed : 23.70 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.65 (0.46), residues: 327 helix: 1.38 (0.37), residues: 178 sheet: -0.74 (0.74), residues: 49 loop : -0.56 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 72 TYR 0.011 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.020 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 2814) covalent geometry : angle 0.56886 / 0.29 ( 3787) SS BOND : bond 0.00708 / 0.37 ( 1) SS BOND : angle 0.87510 / 0.48 ( 2) hydrogen bonds : bond 0.03680 / 2.72 ( 166) hydrogen bonds : angle 4.47103 / 3.18 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7625 (tt0) REVERT: C 43 LYS cc_start: 0.6538 (ttpt) cc_final: 0.6297 (ttpt) REVERT: C 102 TRP cc_start: 0.6149 (t-100) cc_final: 0.5748 (m-90) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.0519 time to fit residues: 4.7835 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.0020 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.193215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157833 restraints weight = 3915.676| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.91 r_work: 0.3764 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2815 Z= 0.117 Angle : 0.516 5.746 3789 Z= 0.265 Chirality : 0.040 0.126 392 Planarity : 0.006 0.062 464 Dihedral : 14.301 76.583 493 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.81 % Allowed : 23.70 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.38 (0.48), residues: 327 helix: 1.98 (0.39), residues: 180 sheet: -1.23 (0.71), residues: 50 loop : 0.24 (0.68), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.010 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.016 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 2814) covalent geometry : angle 0.51569 / 0.27 ( 3787) SS BOND : bond 0.01468 / 0.77 ( 1) SS BOND : angle 0.47794 / 0.26 ( 2) hydrogen bonds : bond 0.03318 / 2.41 ( 166) hydrogen bonds : angle 4.32825 / 3.06 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7595 (tt0) REVERT: A 19 ARG cc_start: 0.7816 (ptt-90) cc_final: 0.6927 (ptt-90) REVERT: C 4 LEU cc_start: 0.7724 (mp) cc_final: 0.7508 (tp) REVERT: C 96 CYS cc_start: 0.5198 (OUTLIER) cc_final: 0.3914 (m) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.0581 time to fit residues: 5.3361 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.0270 chunk 27 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161077 restraints weight = 3837.781| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.85 r_work: 0.3797 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2815 Z= 0.105 Angle : 0.504 7.035 3789 Z= 0.261 Chirality : 0.039 0.135 392 Planarity : 0.005 0.058 464 Dihedral : 13.223 67.549 493 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.19 % Allowed : 25.19 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.73 (0.49), residues: 327 helix: 2.15 (0.39), residues: 180 sheet: -1.19 (0.79), residues: 43 loop : 0.57 (0.68), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.010 0.001 TYR C 95 PHE 0.010 0.001 PHE A 69 TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 2814) covalent geometry : angle 0.50456 / 0.26 ( 3787) SS BOND : bond 0.00411 / 0.22 ( 1) SS BOND : angle 0.28446 / 0.15 ( 2) hydrogen bonds : bond 0.03236 / 2.34 ( 166) hydrogen bonds : angle 4.22105 / 2.98 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7605 (tt0) REVERT: A 19 ARG cc_start: 0.7824 (ptt-90) cc_final: 0.7002 (ptt-90) REVERT: C 43 LYS cc_start: 0.6359 (ttpt) cc_final: 0.6147 (ttpt) REVERT: C 81 LEU cc_start: 0.7546 (tp) cc_final: 0.7023 (mt) REVERT: C 96 CYS cc_start: 0.5124 (OUTLIER) cc_final: 0.4049 (m) REVERT: C 102 TRP cc_start: 0.6282 (t-100) cc_final: 0.5939 (m-90) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0549 time to fit residues: 4.8723 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0609 > 50: distance: 67 - 72: 18.337 distance: 72 - 73: 8.070 distance: 73 - 74: 29.986 distance: 73 - 76: 30.353 distance: 74 - 75: 14.251 distance: 74 - 79: 42.321 distance: 76 - 77: 51.373 distance: 76 - 78: 38.709 distance: 79 - 80: 19.835 distance: 80 - 81: 17.592 distance: 80 - 83: 24.517 distance: 81 - 82: 15.625 distance: 81 - 88: 24.346 distance: 83 - 84: 14.591 distance: 84 - 85: 8.490 distance: 85 - 86: 10.885 distance: 85 - 87: 4.519 distance: 88 - 89: 27.558 distance: 89 - 90: 12.638 distance: 89 - 92: 15.564 distance: 90 - 91: 12.183 distance: 90 - 99: 39.795 distance: 92 - 93: 24.673 distance: 93 - 94: 16.636 distance: 94 - 95: 12.707 distance: 95 - 96: 12.972 distance: 96 - 97: 4.632 distance: 96 - 98: 5.221 distance: 99 - 100: 19.508 distance: 100 - 101: 17.293 distance: 100 - 103: 10.996 distance: 101 - 102: 7.827 distance: 101 - 106: 24.972 distance: 103 - 104: 10.318 distance: 103 - 105: 12.960 distance: 106 - 107: 4.215 distance: 106 - 225: 26.004 distance: 107 - 108: 11.636 distance: 107 - 110: 17.509 distance: 108 - 109: 11.787 distance: 108 - 114: 28.049 distance: 109 - 222: 17.801 distance: 110 - 111: 15.159 distance: 111 - 112: 23.121 distance: 112 - 113: 23.572 distance: 114 - 115: 26.456 distance: 114 - 322: 19.486 distance: 115 - 116: 34.783 distance: 115 - 118: 19.606 distance: 116 - 117: 18.933 distance: 116 - 126: 42.301 distance: 117 - 319: 35.411 distance: 118 - 119: 12.315 distance: 119 - 120: 17.158 distance: 119 - 121: 5.706 distance: 120 - 122: 20.148 distance: 121 - 123: 9.410 distance: 122 - 124: 14.169 distance: 123 - 124: 10.434 distance: 124 - 125: 8.638 distance: 126 - 127: 25.042 distance: 126 - 215: 31.782 distance: 127 - 128: 32.393 distance: 127 - 130: 20.968 distance: 128 - 129: 12.076 distance: 128 - 140: 18.212 distance: 129 - 212: 25.051 distance: 130 - 131: 14.273 distance: 131 - 132: 8.875 distance: 131 - 133: 8.013 distance: 132 - 134: 3.031 distance: 133 - 135: 3.838 distance: 135 - 137: 4.500 distance: 136 - 138: 6.921 distance: 138 - 139: 4.702 distance: 140 - 141: 18.758 distance: 140 - 304: 11.307 distance: 141 - 142: 9.385 distance: 141 - 144: 17.690 distance: 142 - 143: 13.235 distance: 142 - 152: 30.901 distance: 143 - 301: 28.161 distance: 144 - 145: 5.919 distance: 145 - 146: 6.112 distance: 145 - 147: 5.131 distance: 146 - 148: 14.589 distance: 147 - 149: 9.356 distance: 148 - 150: 9.766 distance: 149 - 150: 8.711 distance: 150 - 151: 9.196 distance: 152 - 153: 27.151 distance: 153 - 154: 18.664 distance: 153 - 156: 39.869 distance: 154 - 155: 26.694 distance: 154 - 163: 16.576 distance: 156 - 157: 34.356 distance: 157 - 158: 8.562 distance: 158 - 159: 7.670 distance: 159 - 160: 3.710 distance: 163 - 164: 45.359 distance: 163 - 286: 27.144 distance: 164 - 165: 32.176 distance: 164 - 167: 40.999 distance: 165 - 166: 32.116 distance: 165 - 172: 27.194 distance: 166 - 283: 32.747 distance: 167 - 168: 29.121 distance: 168 - 169: 8.069 distance: 169 - 170: 12.370 distance: 169 - 171: 16.401