Starting phenix.real_space_refine on Wed Jun 11 15:25:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.map" model { file = "/net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nh9_12321/06_2025/7nh9_12321.cif" } resolution = 3.03 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= 0.001 sd= 0.009 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 30 5.16 5 C 8320 2.51 5 N 2375 2.21 5 O 2395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13120 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2624 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.94, per 1000 atoms: 0.45 Number of scatterers: 13120 At special positions: 0 Unit cell: (122.672, 122.016, 126.608, 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 30 16.00 O 2395 8.00 N 2375 7.00 C 8320 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: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 56.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.876A pdb=" N ASP A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 228 through 289 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 313 through 331 removed outlier: 3.650A pdb=" N GLY A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 219 removed outlier: 3.932A pdb=" N TYR B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.876A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 228 through 289 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 313 through 331 removed outlier: 3.650A pdb=" N GLY B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Proline residue: C 208 - end of helix removed outlier: 3.876A pdb=" N ASP C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 228 through 289 Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 removed outlier: 3.535A pdb=" N GLN D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 182 removed outlier: 3.701A pdb=" N THR D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Proline residue: D 208 - end of helix removed outlier: 3.876A pdb=" N ASP D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 228 through 289 Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.536A pdb=" N GLN E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 Processing helix chain 'E' and resid 127 through 139 removed outlier: 3.899A pdb=" N ALA E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 182 removed outlier: 3.700A pdb=" N THR E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 219 removed outlier: 3.931A pdb=" N TYR E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Proline residue: E 208 - end of helix removed outlier: 3.875A pdb=" N ASP E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 228 through 289 Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 313 through 331 removed outlier: 3.651A pdb=" N GLY E 317 " --> pdb=" O LEU E 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS A 46 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 15 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP A 44 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS B 46 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY B 15 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP B 44 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.560A pdb=" N HIS C 46 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY C 15 " --> pdb=" O TRP C 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP C 44 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS D 46 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY D 15 " --> pdb=" O TRP D 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP D 44 " --> pdb=" O GLY D 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.559A pdb=" N HIS E 46 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY E 15 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TRP E 44 " --> pdb=" O GLY E 15 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2340 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: 3.41 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4510 1.34 - 1.46: 2651 1.46 - 1.58: 6174 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13385 Sorted by residual: bond pdb=" C THR A 77 " pdb=" N ARG A 78 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.59e-02 3.96e+03 9.82e+00 bond pdb=" C THR C 77 " pdb=" N ARG C 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.65e+00 bond pdb=" C THR B 77 " pdb=" N ARG B 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.64e+00 bond pdb=" C THR E 77 " pdb=" N ARG E 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.58e+00 bond pdb=" C THR D 77 " pdb=" N ARG D 78 " ideal model delta sigma weight residual 1.331 1.282 0.049 1.59e-02 3.96e+03 9.55e+00 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 17185 1.51 - 3.03: 752 3.03 - 4.54: 138 4.54 - 6.06: 60 6.06 - 7.57: 15 Bond angle restraints: 18150 Sorted by residual: angle pdb=" C ARG E 218 " pdb=" N TYR E 219 " pdb=" CA TYR E 219 " ideal model delta sigma weight residual 121.90 116.20 5.70 1.26e+00 6.30e-01 2.05e+01 angle pdb=" C ARG A 218 " pdb=" N TYR A 219 " pdb=" CA TYR A 219 " ideal model delta sigma weight residual 121.90 116.21 5.69 1.26e+00 6.30e-01 2.04e+01 angle pdb=" C ARG D 218 " pdb=" N TYR D 219 " pdb=" CA TYR D 219 " ideal model delta sigma weight residual 121.90 116.22 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C ARG C 218 " pdb=" N TYR C 219 " pdb=" CA TYR C 219 " ideal model delta sigma weight residual 121.90 116.22 5.68 1.26e+00 6.30e-01 2.03e+01 angle pdb=" C ARG B 218 " pdb=" N TYR B 219 " pdb=" CA TYR B 219 " ideal model delta sigma weight residual 121.90 116.24 5.66 1.26e+00 6.30e-01 2.02e+01 ... (remaining 18145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7160 17.92 - 35.84: 640 35.84 - 53.77: 165 53.77 - 71.69: 10 71.69 - 89.61: 15 Dihedral angle restraints: 7990 sinusoidal: 3310 harmonic: 4680 Sorted by residual: dihedral pdb=" CA LEU C 84 " pdb=" C LEU C 84 " pdb=" N GLY C 85 " pdb=" CA GLY C 85 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU E 84 " pdb=" C LEU E 84 " pdb=" N GLY E 85 " pdb=" CA GLY E 85 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU B 84 " pdb=" C LEU B 84 " pdb=" N GLY B 85 " pdb=" CA GLY B 85 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1029 0.027 - 0.054: 577 0.054 - 0.081: 208 0.081 - 0.108: 136 0.108 - 0.135: 40 Chirality restraints: 1990 Sorted by residual: chirality pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" C PRO B 39 " pdb=" CB PRO B 39 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO E 39 " pdb=" N PRO E 39 " pdb=" C PRO E 39 " pdb=" CB PRO E 39 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1987 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 207 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO E 208 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 208 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 207 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 208 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 208 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " -0.029 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2722 2.77 - 3.30: 13245 3.30 - 3.83: 22022 3.83 - 4.37: 25326 4.37 - 4.90: 43650 Nonbonded interactions: 106965 Sorted by model distance: nonbonded pdb=" OE2 GLU A 244 " pdb=" NH1 ARG E 78 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASN C 97 " pdb=" ND2 ASN C 99 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN B 97 " pdb=" ND2 ASN B 99 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN A 97 " pdb=" ND2 ASN A 99 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN E 97 " pdb=" ND2 ASN E 99 " model vdw 2.249 3.120 ... (remaining 106960 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' 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: 4.220 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.007 0.061 13385 Z= 0.293 Angle : 0.798 7.570 18150 Z= 0.455 Chirality : 0.043 0.135 1990 Planarity : 0.004 0.051 2370 Dihedral : 14.804 89.611 4990 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 3.31 % Allowed : 8.16 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.19), residues: 1625 helix: -0.51 (0.16), residues: 920 sheet: -1.87 (0.32), residues: 230 loop : -3.31 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 57 HIS 0.003 0.001 HIS C 190 PHE 0.009 0.001 PHE A 92 TYR 0.012 0.001 TYR D 151 ARG 0.005 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.13712 ( 795) hydrogen bonds : angle 5.57678 ( 2340) covalent geometry : bond 0.00683 (13385) covalent geometry : angle 0.79844 (18150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.465 Fit side-chains REVERT: A 270 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7889 (ttp-110) REVERT: B 270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7952 (ttp-110) REVERT: C 266 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7702 (pp20) REVERT: C 270 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7943 (ttp-110) REVERT: C 285 MET cc_start: 0.8524 (tpt) cc_final: 0.8205 (tpp) REVERT: C 322 GLN cc_start: 0.7832 (mt0) cc_final: 0.7403 (mt0) REVERT: D 128 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8296 (mmmt) REVERT: D 233 ASN cc_start: 0.9178 (t0) cc_final: 0.8961 (t0) REVERT: D 285 MET cc_start: 0.8453 (tpt) cc_final: 0.8243 (tpp) REVERT: E 270 ARG cc_start: 0.8144 (tpp-160) cc_final: 0.7894 (ttp-110) outliers start: 45 outliers final: 20 residues processed: 217 average time/residue: 0.2425 time to fit residues: 76.7401 Evaluate side-chains 144 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 50.0000 chunk 145 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 209 GLN A 242 ASN A 257 GLN A 322 GLN B 190 HIS B 209 GLN B 242 ASN B 257 GLN B 322 GLN C 190 HIS C 209 GLN C 242 ASN C 257 GLN D 190 HIS D 209 GLN D 242 ASN D 257 GLN D 322 GLN E 190 HIS E 209 GLN E 242 ASN E 257 GLN E 322 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078271 restraints weight = 29148.763| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.98 r_work: 0.3075 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13385 Z= 0.190 Angle : 0.716 9.639 18150 Z= 0.360 Chirality : 0.043 0.154 1990 Planarity : 0.004 0.064 2370 Dihedral : 6.660 62.598 1882 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.50 % Allowed : 10.44 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.21), residues: 1625 helix: 0.96 (0.17), residues: 925 sheet: -1.29 (0.34), residues: 200 loop : -2.68 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 331 HIS 0.015 0.003 HIS C 190 PHE 0.011 0.001 PHE D 282 TYR 0.010 0.001 TYR B 151 ARG 0.008 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 795) hydrogen bonds : angle 3.81686 ( 2340) covalent geometry : bond 0.00451 (13385) covalent geometry : angle 0.71605 (18150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.459 Fit side-chains REVERT: A 103 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: A 270 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8056 (ttp-110) REVERT: B 270 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8152 (ttp-110) REVERT: C 270 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8119 (ttp-170) REVERT: D 128 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7954 (mmmt) REVERT: D 233 ASN cc_start: 0.9197 (t0) cc_final: 0.8977 (t0) REVERT: D 270 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8249 (ttp-110) REVERT: E 270 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8055 (ttp-170) outliers start: 34 outliers final: 16 residues processed: 170 average time/residue: 0.2460 time to fit residues: 61.3527 Evaluate side-chains 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 ARG Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 322 GLN C 322 GLN D 322 GLN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080312 restraints weight = 29401.545| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.00 r_work: 0.3114 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13385 Z= 0.134 Angle : 0.644 9.040 18150 Z= 0.320 Chirality : 0.040 0.156 1990 Planarity : 0.004 0.052 2370 Dihedral : 6.017 67.000 1873 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.81 % Allowed : 14.19 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.21), residues: 1625 helix: 1.65 (0.17), residues: 935 sheet: -1.84 (0.33), residues: 220 loop : -2.70 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.002 0.001 HIS C 190 PHE 0.011 0.001 PHE E 282 TYR 0.008 0.001 TYR A 14 ARG 0.006 0.000 ARG E 184 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 795) hydrogen bonds : angle 3.47785 ( 2340) covalent geometry : bond 0.00309 (13385) covalent geometry : angle 0.64408 (18150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.456 Fit side-chains REVERT: A 270 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8069 (ttp-170) REVERT: B 270 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8160 (ttp-170) REVERT: B 324 TRP cc_start: 0.8756 (t60) cc_final: 0.8293 (t60) REVERT: C 266 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8072 (tm-30) REVERT: C 270 ARG cc_start: 0.8705 (tpp-160) cc_final: 0.8088 (ttp-110) REVERT: C 324 TRP cc_start: 0.8694 (t60) cc_final: 0.8361 (t60) REVERT: D 128 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7775 (mmmt) REVERT: D 233 ASN cc_start: 0.9182 (t0) cc_final: 0.8959 (t0) REVERT: D 324 TRP cc_start: 0.8768 (t60) cc_final: 0.8357 (t60) REVERT: E 270 ARG cc_start: 0.8669 (tpp-160) cc_final: 0.8093 (ttp-170) outliers start: 11 outliers final: 9 residues processed: 157 average time/residue: 0.2297 time to fit residues: 53.8971 Evaluate side-chains 138 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 92 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 322 GLN B 190 HIS B 322 GLN C 190 HIS C 322 GLN D 322 GLN E 190 HIS E 322 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081898 restraints weight = 29088.043| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.01 r_work: 0.3148 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13385 Z= 0.116 Angle : 0.612 8.871 18150 Z= 0.305 Chirality : 0.039 0.160 1990 Planarity : 0.003 0.039 2370 Dihedral : 5.295 57.924 1865 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.74 % Allowed : 15.22 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.22), residues: 1625 helix: 2.08 (0.17), residues: 935 sheet: -1.90 (0.31), residues: 220 loop : -2.58 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 324 HIS 0.024 0.003 HIS E 190 PHE 0.011 0.001 PHE E 282 TYR 0.018 0.001 TYR D 219 ARG 0.005 0.000 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 795) hydrogen bonds : angle 3.28752 ( 2340) covalent geometry : bond 0.00261 (13385) covalent geometry : angle 0.61156 (18150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.653 Fit side-chains REVERT: A 270 ARG cc_start: 0.8695 (tpp-160) cc_final: 0.8120 (ttp-170) REVERT: A 324 TRP cc_start: 0.8651 (t60) cc_final: 0.8422 (t60) REVERT: B 270 ARG cc_start: 0.8769 (tpp-160) cc_final: 0.8174 (ttp-170) REVERT: B 324 TRP cc_start: 0.8749 (t60) cc_final: 0.8348 (t60) REVERT: C 219 TYR cc_start: 0.7730 (p90) cc_final: 0.7476 (p90) REVERT: C 266 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8028 (tm-30) REVERT: C 270 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8162 (ttp-170) REVERT: C 324 TRP cc_start: 0.8679 (t60) cc_final: 0.8385 (t60) REVERT: D 128 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7755 (mmmt) REVERT: D 219 TYR cc_start: 0.7846 (p90) cc_final: 0.7613 (p90) REVERT: D 233 ASN cc_start: 0.9171 (t0) cc_final: 0.8966 (t0) REVERT: D 324 TRP cc_start: 0.8780 (t60) cc_final: 0.8397 (t60) REVERT: E 266 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7945 (tm-30) REVERT: E 270 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8097 (ttp-170) REVERT: E 324 TRP cc_start: 0.8715 (t60) cc_final: 0.8389 (t60) outliers start: 10 outliers final: 10 residues processed: 160 average time/residue: 0.2490 time to fit residues: 59.3841 Evaluate side-chains 145 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 129 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN C 322 GLN D 190 HIS D 322 GLN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075498 restraints weight = 29420.062| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.99 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 13385 Z= 0.313 Angle : 0.757 9.752 18150 Z= 0.379 Chirality : 0.045 0.165 1990 Planarity : 0.004 0.037 2370 Dihedral : 5.784 53.712 1865 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 2.06 % Allowed : 16.76 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.21), residues: 1625 helix: 1.71 (0.17), residues: 935 sheet: -1.32 (0.34), residues: 200 loop : -2.56 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.022 0.002 HIS D 190 PHE 0.013 0.002 PHE E 321 TYR 0.020 0.002 TYR E 219 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 795) hydrogen bonds : angle 3.64504 ( 2340) covalent geometry : bond 0.00764 (13385) covalent geometry : angle 0.75718 (18150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 2.097 Fit side-chains REVERT: A 260 GLU cc_start: 0.8891 (tp30) cc_final: 0.8523 (tp30) REVERT: A 266 GLU cc_start: 0.8226 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 270 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8099 (ttp-170) REVERT: B 270 ARG cc_start: 0.8747 (tpp-160) cc_final: 0.8126 (ttp-110) REVERT: C 219 TYR cc_start: 0.7928 (p90) cc_final: 0.7639 (p90) REVERT: C 260 GLU cc_start: 0.8882 (tp30) cc_final: 0.8463 (tp30) REVERT: C 270 ARG cc_start: 0.8738 (tpp-160) cc_final: 0.8139 (ttp-170) REVERT: D 128 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8031 (mmmt) REVERT: D 233 ASN cc_start: 0.9268 (t0) cc_final: 0.9060 (t0) REVERT: D 260 GLU cc_start: 0.8897 (tp30) cc_final: 0.8543 (tp30) REVERT: E 219 TYR cc_start: 0.7934 (p90) cc_final: 0.7687 (p90) REVERT: E 270 ARG cc_start: 0.8684 (tpp-160) cc_final: 0.8053 (ttp-170) outliers start: 28 outliers final: 15 residues processed: 157 average time/residue: 0.2471 time to fit residues: 58.7319 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 261 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 322 GLN B 190 HIS B 269 ASN B 322 GLN C 190 HIS C 322 GLN D 190 HIS D 322 GLN E 190 HIS E 322 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.108398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080117 restraints weight = 29533.261| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.02 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13385 Z= 0.124 Angle : 0.654 12.980 18150 Z= 0.320 Chirality : 0.040 0.176 1990 Planarity : 0.003 0.034 2370 Dihedral : 5.077 41.298 1865 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.59 % Allowed : 18.01 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.22), residues: 1625 helix: 2.16 (0.17), residues: 935 sheet: -1.64 (0.32), residues: 210 loop : -2.50 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 324 HIS 0.029 0.003 HIS D 190 PHE 0.012 0.001 PHE E 321 TYR 0.019 0.001 TYR E 219 ARG 0.005 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 795) hydrogen bonds : angle 3.33250 ( 2340) covalent geometry : bond 0.00280 (13385) covalent geometry : angle 0.65423 (18150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.970 Fit side-chains REVERT: A 260 GLU cc_start: 0.8850 (tp30) cc_final: 0.8515 (tp30) REVERT: A 270 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8125 (ttm170) REVERT: A 324 TRP cc_start: 0.8692 (t60) cc_final: 0.8422 (t60) REVERT: B 270 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8169 (ttp-170) REVERT: B 324 TRP cc_start: 0.8751 (t60) cc_final: 0.8309 (t60) REVERT: C 219 TYR cc_start: 0.7810 (p90) cc_final: 0.7462 (p90) REVERT: C 260 GLU cc_start: 0.8858 (tp30) cc_final: 0.8412 (tp30) REVERT: C 270 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8154 (ttp-170) REVERT: C 324 TRP cc_start: 0.8711 (t60) cc_final: 0.8365 (t60) REVERT: D 128 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7758 (mmmt) REVERT: D 233 ASN cc_start: 0.9206 (t0) cc_final: 0.9005 (t0) REVERT: E 219 TYR cc_start: 0.7868 (p90) cc_final: 0.7613 (p90) REVERT: E 260 GLU cc_start: 0.8872 (tp30) cc_final: 0.8379 (tp30) REVERT: E 270 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8130 (ttp-170) REVERT: E 324 TRP cc_start: 0.8768 (t60) cc_final: 0.8386 (t60) outliers start: 8 outliers final: 6 residues processed: 154 average time/residue: 0.2578 time to fit residues: 59.2520 Evaluate side-chains 143 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 56.0243 > 50: distance: 14 - 19: 13.912 distance: 19 - 20: 13.715 distance: 20 - 21: 8.823 distance: 20 - 23: 11.570 distance: 21 - 22: 6.480 distance: 21 - 30: 6.335 distance: 23 - 24: 19.079 distance: 24 - 25: 19.035 distance: 25 - 26: 9.989 distance: 26 - 27: 15.626 distance: 27 - 28: 3.299 distance: 27 - 29: 4.553 distance: 30 - 31: 37.157 distance: 31 - 32: 9.104 distance: 32 - 33: 36.841 distance: 32 - 34: 45.949 distance: 34 - 35: 33.187 distance: 35 - 36: 50.050 distance: 35 - 38: 34.949 distance: 36 - 37: 20.141 distance: 36 - 41: 28.206 distance: 38 - 39: 23.266 distance: 38 - 40: 5.359 distance: 41 - 42: 19.225 distance: 42 - 43: 18.320 distance: 42 - 45: 3.563 distance: 43 - 44: 34.208 distance: 43 - 49: 23.451 distance: 45 - 46: 19.515 distance: 46 - 47: 12.575 distance: 46 - 48: 12.407 distance: 49 - 50: 30.204 distance: 50 - 51: 27.750 distance: 50 - 53: 38.916 distance: 51 - 52: 18.586 distance: 51 - 57: 3.894 distance: 53 - 54: 16.559 distance: 54 - 55: 35.254 distance: 54 - 56: 28.575 distance: 57 - 58: 16.411 distance: 58 - 59: 7.950 distance: 58 - 61: 13.124 distance: 59 - 60: 32.013 distance: 59 - 65: 17.084 distance: 61 - 62: 41.688 distance: 62 - 64: 52.656 distance: 65 - 66: 19.858 distance: 65 - 71: 13.748 distance: 66 - 67: 20.336 distance: 66 - 69: 11.107 distance: 67 - 68: 44.084 distance: 67 - 72: 19.453 distance: 69 - 70: 20.792 distance: 70 - 71: 27.918 distance: 72 - 73: 27.465 distance: 73 - 74: 17.640 distance: 74 - 75: 5.262 distance: 74 - 76: 30.310 distance: 76 - 77: 7.193 distance: 77 - 78: 3.229 distance: 77 - 80: 17.559 distance: 78 - 79: 17.055 distance: 78 - 81: 34.605 distance: 81 - 82: 35.175 distance: 82 - 83: 8.124 distance: 82 - 85: 28.573 distance: 83 - 84: 9.299 distance: 83 - 90: 28.927 distance: 85 - 86: 18.537 distance: 86 - 87: 15.369 distance: 87 - 88: 17.762 distance: 87 - 89: 17.356