Starting phenix.real_space_refine on Thu Jan 16 12:08:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqi_33397/01_2025/7xqi_33397.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 48 5.16 5 C 6396 2.51 5 N 1518 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1597 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.68, per 1000 atoms: 0.38 Number of scatterers: 9582 At special positions: 0 Unit cell: (102.608, 106, 103.456, 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 48 16.00 O 1620 8.00 N 1518 7.00 C 6396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 74.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 86 through 112 removed outlier: 3.728A pdb=" N GLU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 177 Processing helix chain 'B' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.802A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 86 through 112 removed outlier: 3.726A pdb=" N GLU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 177 Processing helix chain 'C' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 19 through 31 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 177 Processing helix chain 'D' and resid 204 through 233 removed outlier: 3.598A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.524A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.703A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 177 Processing helix chain 'E' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.523A pdb=" N GLY F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.704A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.803A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 86 through 112 removed outlier: 3.727A pdb=" N GLU F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 Processing helix chain 'F' and resid 204 through 233 removed outlier: 3.597A pdb=" N ILE F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.516A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.515A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1911 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: 2.55 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2826 1.34 - 1.46: 2233 1.46 - 1.58: 4703 1.58 - 1.69: 6 1.69 - 1.81: 60 Bond restraints: 9828 Sorted by residual: bond pdb=" CA TYR E 17 " pdb=" CB TYR E 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.85e+00 bond pdb=" CA TYR F 17 " pdb=" CB TYR F 17 " ideal model delta sigma weight residual 1.531 1.599 -0.069 3.12e-02 1.03e+03 4.83e+00 bond pdb=" CA TYR B 17 " pdb=" CB TYR B 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.76e+00 bond pdb=" CA TYR A 17 " pdb=" CB TYR A 17 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.75e+00 bond pdb=" CA TYR C 17 " pdb=" CB TYR C 17 " ideal model delta sigma weight residual 1.531 1.598 -0.068 3.12e-02 1.03e+03 4.72e+00 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12951 1.77 - 3.54: 303 3.54 - 5.31: 24 5.31 - 7.08: 18 7.08 - 8.85: 12 Bond angle restraints: 13308 Sorted by residual: angle pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 121.19 127.65 -6.46 1.59e+00 3.96e-01 1.65e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 121.19 127.63 -6.44 1.59e+00 3.96e-01 1.64e+01 ... (remaining 13303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 5063 14.30 - 28.60: 435 28.60 - 42.89: 163 42.89 - 57.19: 42 57.19 - 71.49: 36 Dihedral angle restraints: 5739 sinusoidal: 2289 harmonic: 3450 Sorted by residual: dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 793 0.028 - 0.056: 469 0.056 - 0.084: 182 0.084 - 0.113: 46 0.113 - 0.141: 34 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA ARG C 202 " pdb=" N ARG C 202 " pdb=" C ARG C 202 " pdb=" CB ARG C 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ARG F 202 " pdb=" N ARG F 202 " pdb=" C ARG F 202 " pdb=" CB ARG F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VAL B 14 " pdb=" N VAL B 14 " pdb=" C VAL B 14 " pdb=" CB VAL B 14 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1521 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 167 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL C 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL C 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 167 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C VAL D 167 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL D 167 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 168 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 167 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C VAL A 167 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 167 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 168 " 0.009 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 78 2.60 - 3.18: 7583 3.18 - 3.75: 14376 3.75 - 4.33: 17550 4.33 - 4.90: 29760 Nonbonded interactions: 69347 Sorted by model distance: nonbonded pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 61 " pdb=" SG CYS C 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS E 61 " pdb=" SG CYS E 192 " model vdw 2.031 3.760 ... (remaining 69342 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.150 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9828 Z= 0.362 Angle : 0.716 8.849 13308 Z= 0.421 Chirality : 0.043 0.141 1524 Planarity : 0.005 0.028 1608 Dihedral : 14.155 71.487 3498 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.27 % Allowed : 7.39 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1152 helix: -1.10 (0.15), residues: 828 sheet: -0.68 (0.55), residues: 102 loop : -2.78 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 25 HIS 0.001 0.000 HIS F 95 PHE 0.011 0.001 PHE C 52 TYR 0.016 0.002 TYR C 17 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 100 MET cc_start: 0.8049 (tmm) cc_final: 0.7741 (tmm) REVERT: B 166 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9033 (mm-30) REVERT: B 231 VAL cc_start: 0.8127 (p) cc_final: 0.7762 (p) REVERT: C 166 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8978 (mm-30) REVERT: C 213 MET cc_start: 0.9159 (mmm) cc_final: 0.8923 (mmm) REVERT: F 166 GLU cc_start: 0.9241 (mm-30) cc_final: 0.9030 (mm-30) outliers start: 24 outliers final: 7 residues processed: 204 average time/residue: 0.2436 time to fit residues: 67.6083 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain F residue 98 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.100449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.070114 restraints weight = 25731.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072607 restraints weight = 11761.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074041 restraints weight = 7877.315| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9828 Z= 0.174 Angle : 0.544 5.612 13308 Z= 0.286 Chirality : 0.037 0.181 1524 Planarity : 0.003 0.024 1608 Dihedral : 4.899 40.968 1280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.46 % Allowed : 13.64 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1152 helix: 1.33 (0.18), residues: 828 sheet: 2.76 (0.57), residues: 60 loop : -2.98 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 25 HIS 0.002 0.000 HIS A 194 PHE 0.008 0.001 PHE A 52 TYR 0.008 0.001 TYR A 177 ARG 0.001 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8217 (tmm) cc_final: 0.7851 (tmm) REVERT: A 148 ARG cc_start: 0.4026 (mtt-85) cc_final: 0.2923 (tpt170) REVERT: A 227 GLU cc_start: 0.8712 (tp30) cc_final: 0.8205 (tm-30) REVERT: C 166 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8658 (tp30) REVERT: C 187 CYS cc_start: 0.8080 (t) cc_final: 0.7736 (t) REVERT: C 213 MET cc_start: 0.9130 (mmm) cc_final: 0.8827 (mmm) REVERT: C 227 GLU cc_start: 0.8773 (tp30) cc_final: 0.8431 (tm-30) REVERT: D 166 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8691 (tp30) REVERT: D 187 CYS cc_start: 0.8043 (t) cc_final: 0.7575 (t) REVERT: D 227 GLU cc_start: 0.8848 (tp30) cc_final: 0.8382 (tm-30) REVERT: E 47 ASP cc_start: 0.8429 (p0) cc_final: 0.8217 (p0) REVERT: E 148 ARG cc_start: 0.4300 (mtt-85) cc_final: 0.3178 (tpt170) REVERT: E 187 CYS cc_start: 0.8265 (t) cc_final: 0.7868 (t) REVERT: F 47 ASP cc_start: 0.8251 (p0) cc_final: 0.8020 (p0) REVERT: F 148 ARG cc_start: 0.4598 (mtt-85) cc_final: 0.3418 (tpt170) REVERT: F 187 CYS cc_start: 0.8239 (t) cc_final: 0.7780 (t) REVERT: F 227 GLU cc_start: 0.8579 (tp30) cc_final: 0.8296 (tm-30) outliers start: 26 outliers final: 23 residues processed: 189 average time/residue: 0.1941 time to fit residues: 53.1880 Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068326 restraints weight = 25754.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070743 restraints weight = 11627.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072206 restraints weight = 7696.928| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9828 Z= 0.308 Angle : 0.594 7.877 13308 Z= 0.317 Chirality : 0.039 0.211 1524 Planarity : 0.004 0.028 1608 Dihedral : 5.003 42.564 1280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.79 % Allowed : 17.33 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1152 helix: 1.97 (0.19), residues: 834 sheet: 2.81 (0.58), residues: 60 loop : -2.61 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 25 HIS 0.002 0.000 HIS A 74 PHE 0.019 0.001 PHE B 229 TYR 0.012 0.001 TYR A 177 ARG 0.003 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.231 Fit side-chains REVERT: B 31 ILE cc_start: 0.9395 (tp) cc_final: 0.9170 (tt) REVERT: B 100 MET cc_start: 0.8322 (tmm) cc_final: 0.8085 (tmm) REVERT: B 101 ARG cc_start: 0.8550 (tpp-160) cc_final: 0.8171 (tpp-160) REVERT: C 166 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8902 (mm-30) REVERT: C 213 MET cc_start: 0.9139 (mmm) cc_final: 0.8895 (mmm) REVERT: D 227 GLU cc_start: 0.8832 (tp30) cc_final: 0.8343 (tm-30) REVERT: F 148 ARG cc_start: 0.4492 (mtt-85) cc_final: 0.3400 (tpt170) outliers start: 40 outliers final: 32 residues processed: 176 average time/residue: 0.1918 time to fit residues: 49.3836 Evaluate side-chains 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 32 PHE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.097667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068302 restraints weight = 25066.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070704 restraints weight = 11098.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072093 restraints weight = 7337.329| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9828 Z= 0.240 Angle : 0.566 8.910 13308 Z= 0.302 Chirality : 0.037 0.197 1524 Planarity : 0.003 0.027 1608 Dihedral : 4.855 41.744 1280 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.22 % Allowed : 19.79 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1152 helix: 2.24 (0.19), residues: 834 sheet: 2.52 (0.58), residues: 60 loop : -2.35 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 25 HIS 0.001 0.000 HIS F 74 PHE 0.019 0.001 PHE A 229 TYR 0.009 0.001 TYR B 185 ARG 0.004 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8253 (tmm) cc_final: 0.7916 (tmm) REVERT: A 148 ARG cc_start: 0.4200 (mtt-85) cc_final: 0.2953 (tpt170) REVERT: B 31 ILE cc_start: 0.9402 (tp) cc_final: 0.9162 (tt) REVERT: B 100 MET cc_start: 0.8337 (tmm) cc_final: 0.7995 (tmm) REVERT: B 148 ARG cc_start: 0.4432 (mtt-85) cc_final: 0.3161 (tpt170) REVERT: C 148 ARG cc_start: 0.4524 (mtt-85) cc_final: 0.3452 (tpt170) REVERT: C 187 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7921 (m) REVERT: E 148 ARG cc_start: 0.4386 (mtt-85) cc_final: 0.3184 (tpt170) REVERT: F 148 ARG cc_start: 0.4445 (mtt-85) cc_final: 0.3368 (tpt170) outliers start: 34 outliers final: 28 residues processed: 179 average time/residue: 0.1948 time to fit residues: 50.2801 Evaluate side-chains 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4246 > 50: distance: 85 - 127: 22.831 distance: 123 - 127: 20.476 distance: 127 - 128: 25.215 distance: 129 - 130: 40.427 distance: 129 - 138: 29.845 distance: 131 - 132: 8.266 distance: 132 - 133: 5.265 distance: 132 - 134: 8.584 distance: 133 - 135: 7.165 distance: 135 - 137: 12.084 distance: 138 - 139: 35.629 distance: 139 - 140: 44.503 distance: 139 - 142: 44.534 distance: 140 - 146: 39.127 distance: 143 - 145: 41.064 distance: 146 - 147: 49.046 distance: 147 - 148: 13.094 distance: 147 - 150: 13.079 distance: 148 - 152: 40.118 distance: 153 - 154: 49.137 distance: 154 - 155: 11.611 distance: 154 - 163: 41.190 distance: 156 - 157: 12.010 distance: 157 - 158: 49.669 distance: 158 - 159: 14.681 distance: 159 - 160: 32.916 distance: 160 - 161: 33.077 distance: 160 - 162: 41.125 distance: 163 - 164: 59.347 distance: 163 - 169: 45.432 distance: 164 - 165: 40.241 distance: 165 - 166: 9.385 distance: 165 - 170: 36.010 distance: 167 - 168: 56.640 distance: 170 - 171: 21.646 distance: 171 - 172: 11.338 distance: 171 - 174: 13.411 distance: 172 - 173: 40.071 distance: 172 - 177: 40.447 distance: 173 - 202: 41.352 distance: 174 - 175: 26.506 distance: 177 - 178: 30.556 distance: 178 - 179: 7.836 distance: 178 - 181: 22.832 distance: 179 - 180: 40.489 distance: 180 - 210: 34.935 distance: 181 - 182: 21.632 distance: 182 - 183: 42.380 distance: 183 - 184: 30.802 distance: 183 - 185: 20.369 distance: 186 - 187: 21.247 distance: 187 - 188: 51.580 distance: 187 - 190: 54.433 distance: 188 - 189: 28.491 distance: 188 - 195: 11.388 distance: 189 - 220: 34.425 distance: 190 - 191: 43.171 distance: 191 - 192: 41.036 distance: 192 - 193: 57.313 distance: 193 - 194: 47.995 distance: 196 - 197: 30.839 distance: 197 - 198: 36.337 distance: 197 - 202: 7.827 distance: 198 - 228: 22.221 distance: 202 - 203: 14.665 distance: 203 - 204: 8.585 distance: 203 - 206: 26.696 distance: 204 - 205: 17.472 distance: 204 - 210: 28.495 distance: 205 - 236: 34.431