Starting phenix.real_space_refine on Fri Aug 22 12:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag3_15414/08_2025/8ag3_15414.map" } resolution = 3.47 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= 0.015 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 20 5.16 5 C 1668 2.51 5 N 436 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 2632 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "D" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1316 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Time building chain proxies: 1.03, per 1000 atoms: 0.39 Number of scatterers: 2632 At special positions: 0 Unit cell: (78.49, 64.295, 64.295, 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 20 16.00 O 508 8.00 N 436 7.00 C 1668 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: 0.19 Conformation dependent library (CDL) restraints added in 118.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 16.1% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.778A pdb=" N ASN C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 4.125A pdb=" N ILE D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.238A pdb=" N THR C 72 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 155 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 149 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.619A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 103 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.897A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 127 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.831A pdb=" N CYS D 112 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 145 " --> pdb=" O CYS D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 150 hydrogen bonds defined for protein. 423 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: 0.33 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 852 1.35 - 1.46: 557 1.46 - 1.58: 1237 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 2676 Sorted by residual: bond pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO C 80 " pdb=" CG PRO C 80 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.38e-01 bond pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.45e-02 4.76e+03 7.44e-01 bond pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 bond pdb=" CA LYS D 7 " pdb=" CB LYS D 7 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.68e-02 3.54e+03 4.56e-01 ... (remaining 2671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3542 1.78 - 3.55: 58 3.55 - 5.33: 4 5.33 - 7.11: 5 7.11 - 8.88: 1 Bond angle restraints: 3610 Sorted by residual: angle pdb=" CA GLU C 65 " pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA MET D 43 " pdb=" CB MET D 43 " pdb=" CG MET D 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 121.58 -8.88 3.00e+00 1.11e-01 8.77e+00 angle pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" CD PRO C 80 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta sigma weight residual 110.19 114.05 -3.86 1.62e+00 3.81e-01 5.66e+00 ... (remaining 3605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1299 13.04 - 26.08: 225 26.08 - 39.11: 81 39.11 - 52.15: 37 52.15 - 65.19: 12 Dihedral angle restraints: 1654 sinusoidal: 694 harmonic: 960 Sorted by residual: dihedral pdb=" CA ASP C 128 " pdb=" CB ASP C 128 " pdb=" CG ASP C 128 " pdb=" OD1 ASP C 128 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 83 " pdb=" CB ASP C 83 " pdb=" CG ASP C 83 " pdb=" OD1 ASP C 83 " ideal model delta sinusoidal sigma weight residual -30.00 -87.13 57.13 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " pdb=" CD LYS D 77 " ideal model delta sinusoidal sigma weight residual 60.00 117.48 -57.48 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 238 0.028 - 0.057: 103 0.057 - 0.085: 37 0.085 - 0.113: 28 0.113 - 0.141: 6 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 409 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 79 " -0.088 5.00e-02 4.00e+02 1.33e-01 2.81e+01 pdb=" N PRO C 80 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 121 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 43 " -0.005 2.00e-02 2.50e+03 9.79e-03 9.58e-01 pdb=" C MET D 43 " 0.017 2.00e-02 2.50e+03 pdb=" O MET D 43 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU D 44 " -0.006 2.00e-02 2.50e+03 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 59 2.69 - 3.25: 2329 3.25 - 3.80: 3801 3.80 - 4.35: 5021 4.35 - 4.90: 8610 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" O ASP C 48 " pdb=" ND2 ASN C 52 " model vdw 2.143 3.120 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.232 3.040 nonbonded pdb=" O GLN D 10 " pdb=" OH TYR D 101 " model vdw 2.294 3.040 nonbonded pdb=" N GLU C 44 " pdb=" OE1 GLU C 44 " model vdw 2.344 3.120 nonbonded pdb=" NH1 ARG D 23 " pdb=" O TYR D 106 " model vdw 2.350 3.120 ... (remaining 19815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.570 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.002 0.048 2676 Z= 0.114 Angle : 0.600 8.883 3610 Z= 0.322 Chirality : 0.044 0.141 412 Planarity : 0.007 0.133 458 Dihedral : 17.158 65.191 1030 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 34.74 % Favored : 65.26 % 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: -1.45 (0.47), residues: 318 helix: 2.05 (0.79), residues: 50 sheet: -0.29 (0.51), residues: 112 loop : -2.61 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.009 0.001 TYR D 4 PHE 0.010 0.001 PHE D 15 TRP 0.003 0.001 TRP D 91 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2676) covalent geometry : angle 0.60029 ( 3610) hydrogen bonds : bond 0.13884 ( 113) hydrogen bonds : angle 7.18697 ( 423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: D 106 TYR cc_start: 0.8501 (m-80) cc_final: 0.8225 (m-80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0699 time to fit residues: 8.4237 Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108061 restraints weight = 3651.925| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.55 r_work: 0.3178 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.140 Angle : 0.555 5.950 3610 Z= 0.298 Chirality : 0.044 0.140 412 Planarity : 0.006 0.102 458 Dihedral : 4.442 12.599 350 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.95 % Allowed : 28.90 % Favored : 69.16 % 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: -1.28 (0.48), residues: 318 helix: 2.02 (0.80), residues: 50 sheet: 0.01 (0.54), residues: 102 loop : -2.46 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 60 TYR 0.010 0.002 TYR D 101 PHE 0.012 0.001 PHE C 133 TRP 0.005 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2676) covalent geometry : angle 0.55466 ( 3610) hydrogen bonds : bond 0.04366 ( 113) hydrogen bonds : angle 4.81926 ( 423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.107 Fit side-chains REVERT: C 52 ASN cc_start: 0.7859 (m-40) cc_final: 0.7646 (m110) REVERT: C 71 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (p) REVERT: C 75 PHE cc_start: 0.8241 (m-80) cc_final: 0.7656 (m-80) REVERT: C 119 TYR cc_start: 0.8599 (m-80) cc_final: 0.8377 (m-80) REVERT: D 106 TYR cc_start: 0.8574 (m-80) cc_final: 0.8316 (m-80) REVERT: D 156 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8024 (mm) outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.0659 time to fit residues: 8.2735 Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.133329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108422 restraints weight = 3710.688| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.68 r_work: 0.3156 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.136 Angle : 0.540 6.995 3610 Z= 0.290 Chirality : 0.043 0.142 412 Planarity : 0.005 0.086 458 Dihedral : 4.398 11.471 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.90 % Allowed : 26.95 % Favored : 69.16 % 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: -1.23 (0.48), residues: 318 helix: 2.03 (0.79), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.41 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 60 TYR 0.009 0.001 TYR C 101 PHE 0.013 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2676) covalent geometry : angle 0.53994 ( 3610) hydrogen bonds : bond 0.04230 ( 113) hydrogen bonds : angle 4.62161 ( 423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: C 18 GLU cc_start: 0.7495 (mp0) cc_final: 0.6303 (mp0) REVERT: C 52 ASN cc_start: 0.7869 (m-40) cc_final: 0.7652 (m110) REVERT: C 71 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7735 (p) REVERT: C 75 PHE cc_start: 0.8134 (m-80) cc_final: 0.7527 (m-80) REVERT: C 119 TYR cc_start: 0.8530 (m-80) cc_final: 0.8245 (m-80) REVERT: D 101 TYR cc_start: 0.8513 (m-80) cc_final: 0.8152 (m-80) REVERT: D 106 TYR cc_start: 0.8577 (m-80) cc_final: 0.8292 (m-80) REVERT: D 156 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8008 (mm) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.0593 time to fit residues: 7.7921 Evaluate side-chains 114 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108248 restraints weight = 3704.922| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.58 r_work: 0.3185 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2676 Z= 0.118 Angle : 0.528 7.037 3610 Z= 0.283 Chirality : 0.044 0.142 412 Planarity : 0.005 0.083 458 Dihedral : 4.337 12.450 350 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.55 % Allowed : 25.65 % Favored : 69.81 % 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: -1.14 (0.48), residues: 318 helix: 2.22 (0.80), residues: 50 sheet: 0.06 (0.53), residues: 102 loop : -2.37 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.009 0.001 TYR C 101 PHE 0.011 0.001 PHE C 133 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2676) covalent geometry : angle 0.52775 ( 3610) hydrogen bonds : bond 0.03932 ( 113) hydrogen bonds : angle 4.43780 ( 423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7880 (m-40) cc_final: 0.7660 (m-40) REVERT: C 71 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7766 (p) REVERT: C 75 PHE cc_start: 0.8132 (m-80) cc_final: 0.7572 (m-80) REVERT: C 119 TYR cc_start: 0.8509 (m-80) cc_final: 0.8263 (m-80) REVERT: D 13 LYS cc_start: 0.8550 (tptp) cc_final: 0.8220 (tptm) REVERT: D 101 TYR cc_start: 0.8478 (m-80) cc_final: 0.8088 (m-80) REVERT: D 106 TYR cc_start: 0.8582 (m-80) cc_final: 0.8319 (m-80) REVERT: D 119 TYR cc_start: 0.7651 (m-10) cc_final: 0.7188 (m-80) REVERT: D 129 LYS cc_start: 0.8263 (mmtm) cc_final: 0.8057 (mttm) REVERT: D 156 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8043 (mm) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.0732 time to fit residues: 9.5994 Evaluate side-chains 116 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106064 restraints weight = 3652.053| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.53 r_work: 0.3144 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2676 Z= 0.214 Angle : 0.588 6.534 3610 Z= 0.319 Chirality : 0.045 0.148 412 Planarity : 0.005 0.081 458 Dihedral : 4.742 13.376 350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.19 % Allowed : 26.30 % Favored : 68.51 % 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: -1.32 (0.47), residues: 318 helix: 1.82 (0.78), residues: 50 sheet: -0.01 (0.52), residues: 102 loop : -2.43 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 27 TYR 0.014 0.002 TYR D 101 PHE 0.017 0.002 PHE C 133 TRP 0.009 0.002 TRP D 91 HIS 0.003 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 2676) covalent geometry : angle 0.58840 ( 3610) hydrogen bonds : bond 0.04907 ( 113) hydrogen bonds : angle 4.77159 ( 423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 52 ASN cc_start: 0.7987 (m-40) cc_final: 0.7766 (m-40) REVERT: C 60 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7692 (mtp85) REVERT: C 65 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7110 (tm-30) REVERT: C 75 PHE cc_start: 0.8238 (m-80) cc_final: 0.7625 (m-80) REVERT: C 119 TYR cc_start: 0.8612 (m-80) cc_final: 0.8401 (m-80) REVERT: C 140 LYS cc_start: 0.8285 (tttp) cc_final: 0.7797 (tttp) REVERT: D 69 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7561 (mm) REVERT: D 77 LYS cc_start: 0.7802 (pttt) cc_final: 0.7211 (pttm) REVERT: D 156 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8116 (mm) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 0.0724 time to fit residues: 9.6849 Evaluate side-chains 124 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.131586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107479 restraints weight = 3675.146| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.57 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.141 Angle : 0.548 7.194 3610 Z= 0.294 Chirality : 0.044 0.141 412 Planarity : 0.005 0.080 458 Dihedral : 4.511 13.449 350 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.90 % Allowed : 27.60 % Favored : 68.51 % 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: -1.21 (0.47), residues: 318 helix: 2.03 (0.78), residues: 50 sheet: 0.03 (0.53), residues: 102 loop : -2.38 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 27 TYR 0.013 0.002 TYR D 101 PHE 0.014 0.001 PHE C 133 TRP 0.007 0.002 TRP D 91 HIS 0.002 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2676) covalent geometry : angle 0.54757 ( 3610) hydrogen bonds : bond 0.04262 ( 113) hydrogen bonds : angle 4.56370 ( 423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: C 43 MET cc_start: 0.4259 (tpp) cc_final: 0.3739 (tmm) REVERT: C 52 ASN cc_start: 0.7940 (m-40) cc_final: 0.7691 (m-40) REVERT: C 65 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 71 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (p) REVERT: C 75 PHE cc_start: 0.8227 (m-80) cc_final: 0.7584 (m-80) REVERT: C 119 TYR cc_start: 0.8584 (m-80) cc_final: 0.8332 (m-80) REVERT: C 140 LYS cc_start: 0.8267 (tttp) cc_final: 0.7723 (tttp) REVERT: D 19 PHE cc_start: 0.8519 (m-80) cc_final: 0.8317 (m-80) REVERT: D 70 ASP cc_start: 0.8170 (t70) cc_final: 0.7899 (t70) REVERT: D 77 LYS cc_start: 0.7784 (pttt) cc_final: 0.7195 (pttm) REVERT: D 156 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 12 outliers final: 7 residues processed: 110 average time/residue: 0.0708 time to fit residues: 9.0708 Evaluate side-chains 115 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 71.7253 > 50: distance: 2 - 206: 32.280 distance: 14 - 190: 32.877 distance: 17 - 187: 27.463 distance: 26 - 174: 35.866 distance: 109 - 198: 19.689 distance: 112 - 195: 31.276 distance: 122 - 182: 33.999 distance: 125 - 179: 34.233 distance: 166 - 171: 28.415 distance: 171 - 172: 45.632 distance: 172 - 173: 21.186 distance: 172 - 175: 29.691 distance: 173 - 174: 55.602 distance: 173 - 179: 57.311 distance: 175 - 176: 53.999 distance: 176 - 177: 56.133 distance: 176 - 178: 14.334 distance: 180 - 181: 35.413 distance: 181 - 182: 34.259 distance: 181 - 187: 8.581 distance: 183 - 184: 57.117 distance: 184 - 186: 57.586 distance: 187 - 188: 8.012 distance: 188 - 189: 25.447 distance: 189 - 190: 34.288 distance: 189 - 195: 8.082 distance: 191 - 192: 39.742 distance: 193 - 194: 30.060 distance: 195 - 196: 51.009 distance: 196 - 197: 36.559 distance: 196 - 199: 38.983 distance: 197 - 198: 22.066 distance: 197 - 206: 40.715 distance: 199 - 200: 26.212 distance: 202 - 204: 21.204 distance: 203 - 205: 7.653 distance: 204 - 205: 14.347 distance: 206 - 207: 51.396 distance: 207 - 210: 57.191 distance: 208 - 209: 39.700 distance: 208 - 211: 39.760 distance: 211 - 212: 41.382 distance: 212 - 213: 44.393 distance: 212 - 215: 55.802 distance: 213 - 214: 59.444 distance: 213 - 220: 21.294 distance: 215 - 216: 46.315 distance: 216 - 217: 45.692 distance: 217 - 218: 7.670 distance: 218 - 219: 47.383 distance: 221 - 222: 39.521 distance: 221 - 224: 40.608 distance: 222 - 227: 17.819 distance: 224 - 225: 31.993 distance: 227 - 228: 5.348 distance: 228 - 229: 49.128 distance: 228 - 231: 17.829 distance: 229 - 230: 18.368 distance: 231 - 232: 39.931 distance: 235 - 236: 50.356 distance: 236 - 237: 12.666 distance: 236 - 239: 21.122 distance: 239 - 240: 10.512 distance: 240 - 242: 40.248 distance: 244 - 247: 40.761 distance: 245 - 254: 34.761 distance: 248 - 249: 42.038 distance: 249 - 251: 15.465 distance: 251 - 253: 47.586