Starting phenix.real_space_refine on Fri Aug 22 15:38:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0k_24107/08_2025/7n0k_24107.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.073 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 3404 2.51 5 N 852 2.21 5 O 868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5154 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2577 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: A Time building chain proxies: 1.88, per 1000 atoms: 0.36 Number of scatterers: 5154 At special positions: 0 Unit cell: (97.85, 91.67, 90.64, 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 868 8.00 N 852 7.00 C 3404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 206.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 9 through 68 removed outlier: 4.273A pdb=" N TRP B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 101 removed outlier: 3.907A pdb=" N ALA B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.698A pdb=" N ILE B 177 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.079A pdb=" N VAL B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS B 218 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 250 removed outlier: 3.968A pdb=" N PHE B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 335 removed outlier: 3.857A pdb=" N MET B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 3.585A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 68 removed outlier: 4.273A pdb=" N TRP A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 101 removed outlier: 3.906A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.699A pdb=" N ILE A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.078A pdb=" N VAL A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.967A pdb=" N PHE A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 335 removed outlier: 3.858A pdb=" N MET A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 3.584A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.61 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: 1576 1.34 - 1.46: 1379 1.46 - 1.58: 2297 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5296 Sorted by residual: bond pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TRP A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.61e-01 bond pdb=" C TRP B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.52e-01 bond pdb=" N GLY A 213 " pdb=" CA GLY A 213 " ideal model delta sigma weight residual 1.455 1.447 0.008 1.05e-02 9.07e+03 5.51e-01 ... (remaining 5291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7005 1.53 - 3.07: 133 3.07 - 4.60: 18 4.60 - 6.14: 4 6.14 - 7.67: 4 Bond angle restraints: 7164 Sorted by residual: angle pdb=" CA GLN B 124 " pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLN A 124 " pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " pdb=" CD GLN A 124 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.70e+00 3.46e-01 3.99e+00 angle pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " pdb=" CD GLN B 124 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.70e+00 3.46e-01 3.93e+00 angle pdb=" CA LEU A 120 " pdb=" CB LEU A 120 " pdb=" CG LEU A 120 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 ... (remaining 7159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2586 17.87 - 35.74: 340 35.74 - 53.62: 92 53.62 - 71.49: 14 71.49 - 89.36: 14 Dihedral angle restraints: 3046 sinusoidal: 1208 harmonic: 1838 Sorted by residual: dihedral pdb=" CA LEU B 120 " pdb=" C LEU B 120 " pdb=" N LEU B 121 " pdb=" CA LEU B 121 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LEU A 120 " pdb=" C LEU A 120 " pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " pdb=" CD GLU A 60 " pdb=" OE1 GLU A 60 " ideal model delta sinusoidal sigma weight residual 0.00 -89.36 89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.050: 203 0.050 - 0.075: 53 0.075 - 0.100: 9 0.100 - 0.125: 9 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA VAL A 112 " pdb=" N VAL A 112 " pdb=" C VAL A 112 " pdb=" CB VAL A 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 769 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 312 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 313 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 312 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 313 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 69 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 70 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.017 5.00e-02 4.00e+02 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1129 2.77 - 3.30: 5182 3.30 - 3.84: 8155 3.84 - 4.37: 9401 4.37 - 4.90: 15378 Nonbonded interactions: 39245 Sorted by model distance: nonbonded pdb=" O LYS A 137 " pdb=" OG1 THR A 141 " model vdw 2.238 3.040 nonbonded pdb=" O LYS B 137 " pdb=" OG1 THR B 141 " model vdw 2.239 3.040 nonbonded pdb=" O GLN A 44 " pdb=" OG1 THR A 48 " model vdw 2.266 3.040 nonbonded pdb=" O GLN B 44 " pdb=" OG1 THR B 48 " model vdw 2.266 3.040 nonbonded pdb=" O GLU A 38 " pdb=" OG1 THR A 41 " model vdw 2.310 3.040 ... (remaining 39240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.003 0.034 5296 Z= 0.135 Angle : 0.558 7.672 7164 Z= 0.320 Chirality : 0.031 0.125 772 Planarity : 0.003 0.035 888 Dihedral : 18.365 89.361 1858 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 7.46 % Allowed : 17.16 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.29), residues: 614 helix: -1.29 (0.18), residues: 526 sheet: None (None), residues: 0 loop : -1.07 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.007 0.001 TYR A 172 PHE 0.007 0.001 PHE B 127 TRP 0.010 0.001 TRP A 210 HIS 0.003 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5296) covalent geometry : angle 0.55769 ( 7164) hydrogen bonds : bond 0.26734 ( 407) hydrogen bonds : angle 7.90380 ( 1215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7238 (t80) cc_final: 0.6972 (t80) REVERT: A 127 PHE cc_start: 0.7398 (t80) cc_final: 0.7135 (t80) REVERT: A 183 ILE cc_start: 0.7261 (mm) cc_final: 0.6926 (mt) REVERT: A 228 MET cc_start: 0.7126 (mtm) cc_final: 0.6891 (ttm) outliers start: 40 outliers final: 22 residues processed: 130 average time/residue: 0.0755 time to fit residues: 12.7804 Evaluate side-chains 90 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 56 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS B 197 HIS B 241 GLN B 286 GLN A 54 GLN A 184 ASN A 196 HIS A 197 HIS A 241 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.204486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163816 restraints weight = 5823.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167531 restraints weight = 3459.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169847 restraints weight = 2554.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171043 restraints weight = 2141.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172007 restraints weight = 1959.453| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5296 Z= 0.134 Angle : 0.569 8.717 7164 Z= 0.291 Chirality : 0.034 0.122 772 Planarity : 0.005 0.057 888 Dihedral : 8.175 85.678 718 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.92 % Allowed : 22.76 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.31), residues: 614 helix: 1.29 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -2.26 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.014 0.001 TYR B 240 PHE 0.014 0.001 PHE B 195 TRP 0.013 0.001 TRP A 192 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5296) covalent geometry : angle 0.56939 ( 7164) hydrogen bonds : bond 0.05104 ( 407) hydrogen bonds : angle 3.66837 ( 1215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.222 Fit side-chains REVERT: B 158 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.6060 (tpt-90) REVERT: B 234 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7237 (mm-40) REVERT: B 291 LEU cc_start: 0.8928 (mm) cc_final: 0.8319 (tt) REVERT: A 87 MET cc_start: 0.7565 (tpp) cc_final: 0.6900 (tpt) REVERT: A 158 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6176 (tpt-90) REVERT: A 267 TRP cc_start: 0.6514 (t-100) cc_final: 0.6212 (t-100) outliers start: 21 outliers final: 10 residues processed: 99 average time/residue: 0.0710 time to fit residues: 9.1804 Evaluate side-chains 79 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.0000 chunk 5 optimal weight: 5.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN A 30 HIS A 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.199919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157641 restraints weight = 5738.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161813 restraints weight = 3158.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164465 restraints weight = 2241.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165808 restraints weight = 1843.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166455 restraints weight = 1662.716| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5296 Z= 0.129 Angle : 0.512 5.975 7164 Z= 0.261 Chirality : 0.034 0.120 772 Planarity : 0.004 0.048 888 Dihedral : 7.133 81.370 703 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.54 % Allowed : 27.61 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.32), residues: 614 helix: 2.00 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.70 (0.63), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.015 0.001 TYR B 240 PHE 0.008 0.001 PHE A 318 TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5296) covalent geometry : angle 0.51248 ( 7164) hydrogen bonds : bond 0.04462 ( 407) hydrogen bonds : angle 3.34779 ( 1215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7503 (t80) cc_final: 0.6296 (m-10) REVERT: B 158 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6084 (tpt-90) REVERT: A 87 MET cc_start: 0.7701 (tpp) cc_final: 0.6973 (tpt) REVERT: A 88 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8151 (mttt) REVERT: A 127 PHE cc_start: 0.7497 (t80) cc_final: 0.6410 (m-10) REVERT: A 158 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6258 (tpt-90) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.0832 time to fit residues: 9.7322 Evaluate side-chains 80 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** 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 = 0.4375 r_free = 0.4375 target = 0.206431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.165692 restraints weight = 5766.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.169101 restraints weight = 3613.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171303 restraints weight = 2742.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172359 restraints weight = 2320.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.172359 restraints weight = 2125.065| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5296 Z= 0.136 Angle : 0.525 8.943 7164 Z= 0.260 Chirality : 0.035 0.136 772 Planarity : 0.004 0.043 888 Dihedral : 5.927 55.528 698 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.97 % Allowed : 27.24 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.32), residues: 614 helix: 2.31 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.85 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.015 0.001 TYR B 240 PHE 0.007 0.001 PHE A 235 TRP 0.013 0.001 TRP B 210 HIS 0.001 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5296) covalent geometry : angle 0.52536 ( 7164) hydrogen bonds : bond 0.04137 ( 407) hydrogen bonds : angle 3.27125 ( 1215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8315 (t) REVERT: B 127 PHE cc_start: 0.7314 (t80) cc_final: 0.6195 (m-10) REVERT: B 158 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6183 (tpt-90) REVERT: B 230 GLN cc_start: 0.7563 (tt0) cc_final: 0.7063 (tt0) REVERT: B 234 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: A 127 PHE cc_start: 0.7425 (t80) cc_final: 0.6351 (m-10) REVERT: A 158 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6269 (tpt-90) REVERT: A 230 GLN cc_start: 0.7387 (tt0) cc_final: 0.7143 (tt0) outliers start: 32 outliers final: 18 residues processed: 96 average time/residue: 0.0729 time to fit residues: 9.3492 Evaluate side-chains 87 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** 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 = 0.4348 r_free = 0.4348 target = 0.203491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.161335 restraints weight = 5820.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165242 restraints weight = 3389.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167716 restraints weight = 2466.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168978 restraints weight = 2045.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170051 restraints weight = 1852.671| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5296 Z= 0.152 Angle : 0.552 7.888 7164 Z= 0.267 Chirality : 0.035 0.132 772 Planarity : 0.003 0.036 888 Dihedral : 5.713 51.323 696 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.97 % Allowed : 29.48 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.33), residues: 614 helix: 2.45 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.018 0.002 TYR B 240 PHE 0.008 0.001 PHE A 235 TRP 0.013 0.001 TRP A 210 HIS 0.001 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5296) covalent geometry : angle 0.55192 ( 7164) hydrogen bonds : bond 0.04194 ( 407) hydrogen bonds : angle 3.29278 ( 1215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 127 PHE cc_start: 0.7314 (t80) cc_final: 0.6243 (m-10) REVERT: B 158 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6306 (tpt-90) REVERT: B 208 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7590 (tp) REVERT: B 230 GLN cc_start: 0.7561 (tt0) cc_final: 0.7088 (tt0) REVERT: B 234 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: A 127 PHE cc_start: 0.7360 (t80) cc_final: 0.6269 (m-10) REVERT: A 158 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6376 (tpt-90) REVERT: A 208 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7661 (tp) REVERT: A 230 GLN cc_start: 0.7432 (tt0) cc_final: 0.7197 (tt0) outliers start: 32 outliers final: 21 residues processed: 96 average time/residue: 0.0701 time to fit residues: 9.0539 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.206056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165047 restraints weight = 5854.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168416 restraints weight = 3575.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170910 restraints weight = 2683.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172177 restraints weight = 2246.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172917 restraints weight = 2030.933| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5296 Z= 0.130 Angle : 0.536 8.842 7164 Z= 0.258 Chirality : 0.034 0.130 772 Planarity : 0.003 0.029 888 Dihedral : 5.435 47.301 696 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.97 % Allowed : 30.22 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.33), residues: 614 helix: 2.58 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.79 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.021 0.001 TYR B 240 PHE 0.008 0.001 PHE A 195 TRP 0.011 0.001 TRP B 210 HIS 0.001 0.000 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5296) covalent geometry : angle 0.53630 ( 7164) hydrogen bonds : bond 0.03871 ( 407) hydrogen bonds : angle 3.14936 ( 1215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (t) REVERT: B 127 PHE cc_start: 0.7220 (t80) cc_final: 0.6085 (m-10) REVERT: B 158 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6085 (tpt-90) REVERT: B 208 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7353 (tp) REVERT: B 230 GLN cc_start: 0.7481 (tt0) cc_final: 0.6979 (tt0) REVERT: B 234 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: B 309 MET cc_start: 0.7604 (tpp) cc_final: 0.7380 (tpp) REVERT: A 58 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8399 (pp) REVERT: A 89 GLU cc_start: 0.7563 (tt0) cc_final: 0.7327 (pt0) REVERT: A 127 PHE cc_start: 0.7326 (t80) cc_final: 0.6213 (m-10) REVERT: A 158 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6166 (tpt-90) REVERT: A 208 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7334 (tp) REVERT: A 304 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5904 (mm-30) REVERT: A 309 MET cc_start: 0.7601 (tpp) cc_final: 0.7371 (tpp) outliers start: 32 outliers final: 18 residues processed: 96 average time/residue: 0.0696 time to fit residues: 8.9635 Evaluate side-chains 91 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.206673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.165391 restraints weight = 5818.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168929 restraints weight = 3592.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171305 restraints weight = 2699.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172554 restraints weight = 2265.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172834 restraints weight = 2049.082| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5296 Z= 0.127 Angle : 0.525 6.716 7164 Z= 0.254 Chirality : 0.034 0.133 772 Planarity : 0.003 0.029 888 Dihedral : 5.044 43.040 694 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.53 % Allowed : 30.22 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.33), residues: 614 helix: 2.69 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.88 (0.60), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.015 0.001 TYR B 240 PHE 0.009 0.001 PHE B 195 TRP 0.011 0.001 TRP B 210 HIS 0.001 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5296) covalent geometry : angle 0.52464 ( 7164) hydrogen bonds : bond 0.03797 ( 407) hydrogen bonds : angle 3.09746 ( 1215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8361 (pp) REVERT: B 118 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8323 (t) REVERT: B 158 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6161 (tpt-90) REVERT: B 208 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7394 (tp) REVERT: B 230 GLN cc_start: 0.7488 (tt0) cc_final: 0.6979 (tt0) REVERT: B 234 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: B 304 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6045 (mm-30) REVERT: A 127 PHE cc_start: 0.7204 (t80) cc_final: 0.6148 (m-10) REVERT: A 158 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6194 (tpt-90) REVERT: A 208 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7404 (tp) REVERT: A 304 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.6219 (mm-30) outliers start: 35 outliers final: 20 residues processed: 96 average time/residue: 0.0788 time to fit residues: 9.7862 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.206381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.165429 restraints weight = 5770.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.168962 restraints weight = 3547.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171020 restraints weight = 2653.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172638 restraints weight = 2242.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.172966 restraints weight = 2013.096| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5296 Z= 0.127 Angle : 0.555 11.269 7164 Z= 0.265 Chirality : 0.034 0.208 772 Planarity : 0.003 0.029 888 Dihedral : 4.839 38.256 694 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.53 % Allowed : 30.78 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.37 (0.33), residues: 614 helix: 2.74 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.023 0.001 TYR B 240 PHE 0.010 0.001 PHE B 195 TRP 0.011 0.001 TRP B 210 HIS 0.001 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5296) covalent geometry : angle 0.55522 ( 7164) hydrogen bonds : bond 0.03712 ( 407) hydrogen bonds : angle 3.05796 ( 1215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 158 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6177 (tpt-90) REVERT: B 208 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7340 (tp) REVERT: B 230 GLN cc_start: 0.7453 (tt0) cc_final: 0.6943 (tt0) REVERT: B 234 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6569 (mp10) REVERT: B 309 MET cc_start: 0.7619 (tpp) cc_final: 0.7356 (tpp) REVERT: A 81 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: A 127 PHE cc_start: 0.7248 (t80) cc_final: 0.6242 (m-10) REVERT: A 158 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6169 (tpt-90) REVERT: A 208 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7330 (tp) REVERT: A 309 MET cc_start: 0.7609 (tpp) cc_final: 0.7288 (tpp) outliers start: 35 outliers final: 23 residues processed: 90 average time/residue: 0.0667 time to fit residues: 8.0697 Evaluate side-chains 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8862 > 50: distance: 32 - 52: 5.132 distance: 38 - 61: 7.714 distance: 43 - 70: 16.067 distance: 46 - 52: 3.311 distance: 47 - 78: 15.123 distance: 52 - 53: 5.645 distance: 53 - 54: 4.418 distance: 53 - 56: 11.248 distance: 54 - 61: 3.608 distance: 55 - 85: 16.444 distance: 56 - 57: 8.025 distance: 57 - 58: 6.666 distance: 58 - 59: 14.356 distance: 58 - 60: 9.632 distance: 61 - 62: 5.963 distance: 62 - 63: 5.443 distance: 62 - 65: 9.898 distance: 63 - 64: 3.894 distance: 63 - 70: 15.621 distance: 64 - 94: 9.590 distance: 65 - 66: 8.441 distance: 66 - 67: 5.531 distance: 67 - 68: 7.756 distance: 67 - 69: 7.835 distance: 70 - 71: 3.822 distance: 71 - 72: 6.371 distance: 71 - 74: 4.509 distance: 72 - 73: 7.665 distance: 72 - 78: 4.236 distance: 73 - 102: 8.726 distance: 74 - 75: 6.831 distance: 75 - 76: 5.976 distance: 75 - 77: 11.231 distance: 78 - 79: 5.591 distance: 79 - 80: 7.162 distance: 79 - 82: 6.214 distance: 80 - 81: 5.035 distance: 80 - 85: 4.086 distance: 81 - 111: 6.169 distance: 82 - 83: 7.751 distance: 82 - 84: 6.682 distance: 85 - 86: 3.084 distance: 86 - 87: 3.288 distance: 86 - 89: 5.510 distance: 87 - 88: 7.351 distance: 88 - 116: 13.189 distance: 89 - 90: 10.723 distance: 90 - 91: 4.708 distance: 91 - 92: 5.585 distance: 92 - 93: 8.416 distance: 94 - 95: 4.871 distance: 95 - 96: 5.681 distance: 95 - 98: 6.343 distance: 96 - 97: 7.070 distance: 96 - 102: 6.826 distance: 97 - 124: 11.080 distance: 98 - 99: 9.588 distance: 99 - 100: 16.646 distance: 99 - 101: 9.714 distance: 102 - 103: 6.187 distance: 103 - 104: 3.312 distance: 103 - 106: 8.257 distance: 104 - 105: 5.805 distance: 105 - 130: 4.149 distance: 106 - 107: 5.605 distance: 107 - 108: 4.254 distance: 108 - 109: 4.499 distance: 111 - 112: 4.841 distance: 112 - 113: 13.982 distance: 112 - 115: 9.993 distance: 113 - 114: 8.970 distance: 113 - 116: 6.685 distance: 114 - 137: 25.008 distance: 116 - 117: 5.372 distance: 117 - 118: 3.553 distance: 117 - 120: 5.368 distance: 118 - 119: 7.647 distance: 118 - 124: 6.873 distance: 119 - 145: 21.213 distance: 120 - 121: 12.128 distance: 121 - 122: 21.489 distance: 121 - 123: 12.838 distance: 124 - 125: 31.261 distance: 125 - 126: 14.891 distance: 125 - 128: 30.165 distance: 126 - 127: 4.921 distance: 126 - 130: 5.201 distance: 127 - 151: 10.280 distance: 128 - 129: 9.351