Starting phenix.real_space_refine on Wed Mar 12 02:47:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2025/6u5h_20646.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 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 42 5.16 5 C 4530 2.51 5 N 1362 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B Time building chain proxies: 4.71, per 1000 atoms: 0.64 Number of scatterers: 7326 At special positions: 0 Unit cell: (90.567, 94.731, 78.075, 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 42 16.00 O 1392 8.00 N 1362 7.00 C 4530 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: 1.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 10.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 177 " --> pdb=" O PRO B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.753A pdb=" N ASP A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.610A pdb=" N GLU A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.994A pdb=" N ARG A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 8 removed outlier: 3.668A pdb=" N GLY C 63 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 73 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 62 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG C 71 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG C 41 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C 25 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 39 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 removed outlier: 5.676A pdb=" N ILE C 303 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN C 322 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY B 63 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 73 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 62 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG B 71 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG B 41 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 25 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE B 303 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 322 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY A 63 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 73 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 62 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 71 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG A 41 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 25 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE A 303 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN A 322 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 202 through 203 81 hydrogen bonds defined for protein. 225 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: 1.59 Time building geometry restraints manager: 1.96 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: 2539 1.34 - 1.46: 1375 1.46 - 1.58: 3460 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 7443 Sorted by residual: bond pdb=" C LEU A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.76e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" CB PRO C 86 " pdb=" CG PRO C 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" C LEU B 218 " pdb=" N PRO B 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.66e+00 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9573 2.10 - 4.20: 387 4.20 - 6.30: 48 6.30 - 8.39: 26 8.39 - 10.49: 19 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N VAL B 14 " pdb=" CA VAL B 14 " pdb=" C VAL B 14 " ideal model delta sigma weight residual 108.95 101.03 7.92 1.65e+00 3.67e-01 2.31e+01 angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 108.95 101.07 7.88 1.65e+00 3.67e-01 2.28e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 108.95 101.09 7.86 1.65e+00 3.67e-01 2.27e+01 angle pdb=" CA PRO A 85 " pdb=" C PRO A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 117.93 123.03 -5.10 1.20e+00 6.94e-01 1.81e+01 angle pdb=" CA PRO B 85 " pdb=" C PRO B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 117.93 123.00 -5.07 1.20e+00 6.94e-01 1.78e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 4254 14.28 - 28.55: 249 28.55 - 42.83: 9 42.83 - 57.10: 0 57.10 - 71.38: 6 Dihedral angle restraints: 4518 sinusoidal: 1830 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE A 199 " pdb=" C PHE A 199 " pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE C 199 " pdb=" C PHE C 199 " pdb=" N ASP C 200 " pdb=" CA ASP C 200 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 824 0.058 - 0.117: 229 0.117 - 0.175: 61 0.175 - 0.233: 8 0.233 - 0.292: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE B 105 " pdb=" CA ILE B 105 " pdb=" CG1 ILE B 105 " pdb=" CG2 ILE B 105 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1122 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 187 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.035 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1109 2.77 - 3.30: 6094 3.30 - 3.83: 11304 3.83 - 4.37: 13014 4.37 - 4.90: 22207 Nonbonded interactions: 53728 Sorted by model distance: nonbonded pdb=" OG1 THR B 79 " pdb=" OG1 THR B 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 79 " pdb=" OG1 THR C 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" OG1 THR A 92 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 104 " pdb=" OG1 THR B 153 " model vdw 2.246 3.040 nonbonded pdb=" O THR C 104 " pdb=" OG1 THR C 153 " model vdw 2.247 3.040 ... (remaining 53723 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.380 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.070 Find NCS groups from input model: 0.140 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 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 : 0.005 0.066 7443 Z= 0.355 Angle : 1.067 10.493 10053 Z= 0.571 Chirality : 0.059 0.292 1125 Planarity : 0.006 0.063 1326 Dihedral : 8.739 71.380 2796 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % Favored : 99.23 % 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: -5.23 (0.22), residues: 942 helix: -5.41 (0.09), residues: 90 sheet: -3.34 (0.32), residues: 213 loop : -3.43 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 315 HIS 0.006 0.002 HIS C 150 PHE 0.011 0.002 PHE A 151 TYR 0.023 0.002 TYR C 310 ARG 0.006 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8442 (p) cc_final: 0.8184 (p) REVERT: C 198 SER cc_start: 0.8614 (p) cc_final: 0.8385 (m) REVERT: C 215 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5761 (mmm160) REVERT: B 44 ASP cc_start: 0.8156 (m-30) cc_final: 0.7889 (m-30) REVERT: B 48 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7931 (mm-40) REVERT: B 64 TYR cc_start: 0.8561 (m-10) cc_final: 0.8121 (m-10) REVERT: B 215 ARG cc_start: 0.6355 (mtt180) cc_final: 0.5448 (mmm160) REVERT: B 289 LEU cc_start: 0.7809 (mt) cc_final: 0.7508 (mt) REVERT: A 205 ASP cc_start: 0.7634 (m-30) cc_final: 0.7286 (m-30) REVERT: A 215 ARG cc_start: 0.6525 (mtt180) cc_final: 0.5844 (mmp-170) REVERT: A 281 ASP cc_start: 0.7677 (m-30) cc_final: 0.7103 (m-30) outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.2804 time to fit residues: 77.3193 Evaluate side-chains 135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS B 81 GLN B 242 HIS A 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.226013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.181746 restraints weight = 7866.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.182465 restraints weight = 7031.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.182962 restraints weight = 6534.752| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7443 Z= 0.282 Angle : 0.769 7.440 10053 Z= 0.392 Chirality : 0.047 0.134 1125 Planarity : 0.006 0.048 1326 Dihedral : 7.189 25.760 1059 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.22 % Allowed : 7.98 % Favored : 88.80 % 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: -5.11 (0.22), residues: 942 helix: -5.13 (0.18), residues: 96 sheet: -3.57 (0.26), residues: 267 loop : -3.08 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.015 0.002 PHE C 265 TYR 0.020 0.002 TYR A 159 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6940 (mmt90) REVERT: C 205 ASP cc_start: 0.7891 (m-30) cc_final: 0.7564 (m-30) REVERT: C 215 ARG cc_start: 0.6477 (mtt180) cc_final: 0.5877 (mmm160) REVERT: C 322 ASN cc_start: 0.7188 (m110) cc_final: 0.6734 (m110) REVERT: B 215 ARG cc_start: 0.6168 (mtt180) cc_final: 0.5492 (mmm160) REVERT: B 302 LEU cc_start: 0.8509 (mt) cc_final: 0.8177 (mt) REVERT: B 322 ASN cc_start: 0.6922 (m110) cc_final: 0.6487 (m110) REVERT: A 120 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6270 (mmt90) REVERT: A 205 ASP cc_start: 0.7761 (m-30) cc_final: 0.7258 (m-30) REVERT: A 215 ARG cc_start: 0.6518 (mtt180) cc_final: 0.5954 (mmm160) REVERT: A 259 LYS cc_start: 0.5925 (mttt) cc_final: 0.5579 (mmtp) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.2303 time to fit residues: 50.3699 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 overall best weight: 2.4944 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.226653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.187481 restraints weight = 8019.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.186323 restraints weight = 10851.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.186115 restraints weight = 9371.123| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7443 Z= 0.213 Angle : 0.709 8.517 10053 Z= 0.356 Chirality : 0.045 0.136 1125 Planarity : 0.005 0.044 1326 Dihedral : 6.669 24.481 1059 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.09 % Allowed : 11.45 % Favored : 85.46 % 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: -4.86 (0.23), residues: 942 helix: -4.85 (0.27), residues: 96 sheet: -3.32 (0.27), residues: 279 loop : -2.95 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 82 HIS 0.003 0.001 HIS A 150 PHE 0.018 0.001 PHE B 265 TYR 0.011 0.001 TYR B 159 ARG 0.005 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 169 MET cc_start: 0.3438 (mmt) cc_final: 0.3077 (mmt) REVERT: C 215 ARG cc_start: 0.6343 (mtt180) cc_final: 0.5900 (mmm160) REVERT: C 322 ASN cc_start: 0.7417 (m110) cc_final: 0.7176 (m-40) REVERT: B 215 ARG cc_start: 0.6150 (mtt180) cc_final: 0.5620 (mmm160) REVERT: B 286 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7273 (mtp180) REVERT: B 310 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: A 120 ARG cc_start: 0.6663 (mtt90) cc_final: 0.6341 (mmt90) REVERT: A 205 ASP cc_start: 0.7784 (m-30) cc_final: 0.7149 (m-30) REVERT: A 215 ARG cc_start: 0.6525 (mtt180) cc_final: 0.6115 (mmm160) REVERT: A 259 LYS cc_start: 0.5957 (mttt) cc_final: 0.5689 (mmtp) REVERT: A 322 ASN cc_start: 0.7090 (m110) cc_final: 0.6765 (m-40) outliers start: 24 outliers final: 17 residues processed: 152 average time/residue: 0.2565 time to fit residues: 49.1909 Evaluate side-chains 147 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 HIS B 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.220427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.186227 restraints weight = 8091.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.181067 restraints weight = 12379.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.178036 restraints weight = 11684.561| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7443 Z= 0.289 Angle : 0.737 8.934 10053 Z= 0.370 Chirality : 0.046 0.139 1125 Planarity : 0.006 0.046 1326 Dihedral : 6.534 24.568 1059 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 3.35 % Allowed : 13.00 % Favored : 83.66 % 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: -4.86 (0.23), residues: 942 helix: -5.02 (0.17), residues: 96 sheet: -3.31 (0.28), residues: 276 loop : -2.92 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 315 HIS 0.004 0.001 HIS A 246 PHE 0.025 0.002 PHE A 265 TYR 0.012 0.002 TYR C 310 ARG 0.006 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 MET cc_start: 0.7095 (mtt) cc_final: 0.6628 (mtt) REVERT: C 215 ARG cc_start: 0.6337 (mtt180) cc_final: 0.5775 (mmm160) REVERT: B 209 MET cc_start: 0.6676 (mtt) cc_final: 0.6441 (mtt) REVERT: B 300 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7609 (tp30) REVERT: B 310 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: A 215 ARG cc_start: 0.6442 (mtt180) cc_final: 0.5867 (mmm160) REVERT: A 259 LYS cc_start: 0.6034 (mttt) cc_final: 0.5731 (mmtp) REVERT: A 310 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: A 322 ASN cc_start: 0.7273 (m110) cc_final: 0.6954 (m-40) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.2361 time to fit residues: 46.4830 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 310 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 40 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.226802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189847 restraints weight = 8034.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.188356 restraints weight = 13011.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.187658 restraints weight = 12078.915| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7443 Z= 0.168 Angle : 0.654 7.334 10053 Z= 0.326 Chirality : 0.044 0.134 1125 Planarity : 0.004 0.041 1326 Dihedral : 6.051 22.142 1059 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.96 % Allowed : 15.96 % Favored : 81.08 % 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: -4.78 (0.23), residues: 942 helix: -5.02 (0.17), residues: 114 sheet: -3.04 (0.27), residues: 300 loop : -2.83 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 82 HIS 0.003 0.001 HIS C 150 PHE 0.012 0.001 PHE B 265 TYR 0.007 0.001 TYR C 216 ARG 0.007 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 215 ARG cc_start: 0.6404 (mtt180) cc_final: 0.5912 (mmm160) REVERT: B 300 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7748 (tp30) REVERT: B 310 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6396 (m-10) REVERT: A 215 ARG cc_start: 0.6376 (mtt180) cc_final: 0.5997 (mmm160) REVERT: A 259 LYS cc_start: 0.5922 (mttt) cc_final: 0.5669 (mmtp) REVERT: A 310 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: A 322 ASN cc_start: 0.7129 (m110) cc_final: 0.6859 (m-40) outliers start: 23 outliers final: 15 residues processed: 165 average time/residue: 0.2426 time to fit residues: 50.5660 Evaluate side-chains 152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 310 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 56.9243 > 50: distance: 12 - 36: 19.817 distance: 24 - 28: 12.793 distance: 28 - 29: 30.129 distance: 29 - 30: 14.007 distance: 29 - 32: 10.883 distance: 30 - 31: 17.064 distance: 30 - 36: 28.709 distance: 32 - 33: 15.088 distance: 33 - 34: 7.502 distance: 33 - 35: 12.141 distance: 36 - 37: 10.989 distance: 37 - 38: 12.615 distance: 37 - 40: 21.098 distance: 38 - 39: 11.132 distance: 38 - 47: 15.864 distance: 40 - 41: 24.113 distance: 41 - 42: 41.854 distance: 42 - 43: 17.409 distance: 43 - 44: 19.308 distance: 44 - 45: 13.056 distance: 44 - 46: 13.732 distance: 47 - 48: 34.258 distance: 48 - 49: 18.529 distance: 48 - 51: 13.924 distance: 49 - 50: 9.773 distance: 49 - 55: 41.197 distance: 52 - 53: 41.276 distance: 52 - 54: 32.743 distance: 55 - 161: 25.686 distance: 56 - 57: 29.123 distance: 56 - 59: 20.512 distance: 57 - 58: 5.044 distance: 57 - 63: 32.503 distance: 59 - 60: 21.764 distance: 60 - 61: 42.161 distance: 60 - 62: 17.257 distance: 63 - 64: 16.401 distance: 64 - 65: 17.106 distance: 64 - 67: 12.607 distance: 65 - 66: 19.061 distance: 65 - 72: 13.574 distance: 67 - 68: 17.125 distance: 68 - 69: 14.050 distance: 69 - 70: 28.229 distance: 70 - 71: 26.534 distance: 72 - 73: 27.997 distance: 73 - 74: 26.245 distance: 73 - 76: 20.883 distance: 74 - 75: 27.217 distance: 74 - 80: 13.493 distance: 76 - 77: 14.458 distance: 77 - 78: 31.619 distance: 77 - 79: 33.052 distance: 80 - 81: 9.160 distance: 81 - 82: 24.727 distance: 81 - 84: 22.353 distance: 82 - 83: 32.121 distance: 82 - 87: 24.451 distance: 84 - 85: 41.069 distance: 84 - 86: 40.941 distance: 87 - 88: 18.052 distance: 88 - 89: 25.034 distance: 88 - 91: 20.428 distance: 89 - 90: 19.954 distance: 89 - 95: 14.773 distance: 91 - 92: 10.793 distance: 92 - 93: 22.399 distance: 92 - 94: 37.435 distance: 95 - 96: 19.135 distance: 96 - 97: 16.726 distance: 96 - 99: 21.301 distance: 97 - 98: 9.218 distance: 97 - 103: 21.307 distance: 99 - 100: 11.449 distance: 100 - 101: 19.543 distance: 100 - 102: 17.031 distance: 103 - 104: 17.228 distance: 104 - 105: 27.952 distance: 104 - 107: 23.835 distance: 105 - 106: 11.003 distance: 105 - 111: 23.956 distance: 107 - 108: 20.005 distance: 108 - 109: 11.060