Starting phenix.real_space_refine on Tue Jun 17 18:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.275 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.map" model { file = "/net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j9j_5778/06_2025/3j9j_5778.cif" } resolution = 3.275 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= 1.000 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 6952 2.51 5 N 1608 2.21 5 O 1804 1.98 5 H 10624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21068 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5267 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308} Restraints were copied for chains: C, B, D Time building chain proxies: 13.15, per 1000 atoms: 0.62 Number of scatterers: 21068 At special positions: 0 Unit cell: (117.913, 117.913, 82.6608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 1804 8.00 N 1608 7.00 C 6952 6.00 H 10624 1.00 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: 7.44 Conformation dependent library (CDL) restraints added in 1.8 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 74 Processing helix chain 'A' and resid 88 through 119 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.772A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 74 Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 130 through 152 removed outlier: 4.390A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.850A pdb=" N PHE B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 287 through 309 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 49 through 74 Processing helix chain 'C' and resid 88 through 119 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 130 through 152 removed outlier: 4.391A pdb=" N PHE C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 206 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.852A pdb=" N PHE C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 268 Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 287 through 309 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 35 through 49 Processing helix chain 'D' and resid 49 through 74 Processing helix chain 'D' and resid 88 through 119 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 130 through 152 removed outlier: 4.392A pdb=" N PHE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 195 through 219 removed outlier: 3.771A pdb=" N VAL D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 206 " --> pdb=" O PHE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.851A pdb=" N PHE D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 268 Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 287 through 309 760 hydrogen bonds defined for protein. 2208 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: 13.74 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10600 1.13 - 1.30: 1564 1.30 - 1.47: 4509 1.47 - 1.64: 4515 1.64 - 1.81: 136 Bond restraints: 21324 Sorted by residual: bond pdb=" CE1 HIS A 30 " pdb=" HE1 HIS A 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 HIS C 30 " pdb=" HE1 HIS C 30 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CE1 TYR B 131 " pdb=" HE1 TYR B 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" CE1 TYR A 131 " pdb=" HE1 TYR A 131 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CZ2 TRP C 294 " pdb=" HZ2 TRP C 294 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 34267 2.66 - 5.32: 3235 5.32 - 7.98: 898 7.98 - 10.64: 8 10.64 - 13.31: 24 Bond angle restraints: 38432 Sorted by residual: angle pdb=" C ARG B 120 " pdb=" N PRO B 121 " pdb=" CA PRO B 121 " ideal model delta sigma weight residual 119.28 127.05 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" C ARG D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta sigma weight residual 119.28 127.04 -7.76 1.10e+00 8.26e-01 4.98e+01 angle pdb=" C ARG A 120 " pdb=" N PRO A 121 " pdb=" CA PRO A 121 " ideal model delta sigma weight residual 119.28 127.01 -7.73 1.10e+00 8.26e-01 4.93e+01 angle pdb=" C ARG C 120 " pdb=" N PRO C 121 " pdb=" CA PRO C 121 " ideal model delta sigma weight residual 119.28 126.97 -7.69 1.10e+00 8.26e-01 4.89e+01 angle pdb=" C LEU D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.03e+00 9.43e-01 4.50e+01 ... (remaining 38427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 9433 13.30 - 26.61: 311 26.61 - 39.91: 68 39.91 - 53.21: 98 53.21 - 66.51: 130 Dihedral angle restraints: 10040 sinusoidal: 5252 harmonic: 4788 Sorted by residual: dihedral pdb=" CB MET D 182 " pdb=" CG MET D 182 " pdb=" SD MET D 182 " pdb=" CE MET D 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.64 -39.64 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET C 182 " pdb=" CG MET C 182 " pdb=" SD MET C 182 " pdb=" CE MET C 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.63 -39.63 3 1.50e+01 4.44e-03 7.03e+00 dihedral pdb=" CB MET A 182 " pdb=" CG MET A 182 " pdb=" SD MET A 182 " pdb=" CE MET A 182 " ideal model delta sinusoidal sigma weight residual 60.00 99.62 -39.62 3 1.50e+01 4.44e-03 7.03e+00 ... (remaining 10037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 566 0.047 - 0.093: 570 0.093 - 0.140: 323 0.140 - 0.186: 106 0.186 - 0.233: 59 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA PHE A 309 " pdb=" N PHE A 309 " pdb=" C PHE A 309 " pdb=" CB PHE A 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE B 309 " pdb=" N PHE B 309 " pdb=" C PHE B 309 " pdb=" CB PHE B 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA PHE D 309 " pdb=" N PHE D 309 " pdb=" C PHE D 309 " pdb=" CB PHE D 309 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1621 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 30 " 0.057 2.00e-02 2.50e+03 4.44e-02 4.43e+01 pdb=" CG HIS D 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS D 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS D 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS D 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS D 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS D 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS D 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS D 30 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 30 " -0.057 2.00e-02 2.50e+03 4.43e-02 4.42e+01 pdb=" CG HIS A 30 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS A 30 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 30 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 30 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 30 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS A 30 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS A 30 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 30 " 0.057 2.00e-02 2.50e+03 4.42e-02 4.40e+01 pdb=" CG HIS B 30 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS B 30 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 30 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS B 30 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS B 30 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 30 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 HIS B 30 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS B 30 " 0.042 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 710 2.01 - 2.66: 28402 2.66 - 3.30: 66390 3.30 - 3.95: 84546 3.95 - 4.60: 128117 Nonbonded interactions: 308165 Sorted by model distance: nonbonded pdb=" OE1 GLU D 156 " pdb=" H GLU D 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU C 156 " pdb=" H GLU C 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU A 156 " pdb=" H GLU A 156 " model vdw 1.360 2.450 nonbonded pdb=" OE1 GLU A 11 " pdb=" H GLU A 11 " model vdw 1.522 2.450 ... (remaining 308160 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 56.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.350 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 63.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:4.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 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 : 0.015 0.063 10700 Z= 0.974 Angle : 1.078 9.580 14452 Z= 0.764 Chirality : 0.089 0.233 1624 Planarity : 0.010 0.126 1756 Dihedral : 9.349 66.513 3880 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 2.24 % Allowed : 3.27 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1252 helix: -0.21 (0.15), residues: 964 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.010 TRP D 294 HIS 0.002 0.001 HIS C 30 PHE 0.023 0.004 PHE A 256 TYR 0.044 0.005 TYR D 250 ARG 0.004 0.001 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.16613 ( 760) hydrogen bonds : angle 5.87144 ( 2208) covalent geometry : bond 0.01484 (10700) covalent geometry : angle 1.07839 (14452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 MET cc_start: 0.5276 (mmm) cc_final: 0.5068 (mmm) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.7332 time to fit residues: 538.8053 Evaluate side-chains 295 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.086206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073352 restraints weight = 104964.604| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.35 r_work: 0.3146 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10700 Z= 0.178 Angle : 0.604 4.742 14452 Z= 0.335 Chirality : 0.036 0.150 1624 Planarity : 0.005 0.069 1756 Dihedral : 4.190 21.642 1408 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.35 % Favored : 94.01 % Rotamer: Outliers : 2.60 % Allowed : 10.76 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1252 helix: 1.26 (0.15), residues: 944 sheet: None (None), residues: 0 loop : -0.25 (0.43), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 169 HIS 0.002 0.001 HIS C 30 PHE 0.011 0.001 PHE D 256 TYR 0.011 0.001 TYR B 21 ARG 0.003 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.06032 ( 760) hydrogen bonds : angle 4.58946 ( 2208) covalent geometry : bond 0.00358 (10700) covalent geometry : angle 0.60360 (14452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 375 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: A 221 ASP cc_start: 0.7864 (t0) cc_final: 0.7456 (m-30) REVERT: A 233 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 181 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: B 221 ASP cc_start: 0.7860 (t0) cc_final: 0.7470 (m-30) REVERT: B 233 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8517 (mm-30) REVERT: B 269 ILE cc_start: 0.9178 (mt) cc_final: 0.8563 (mt) REVERT: C 233 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8543 (mm-30) REVERT: C 302 ILE cc_start: 0.9779 (mt) cc_final: 0.9525 (mt) REVERT: D 204 TYR cc_start: 0.9185 (t80) cc_final: 0.8890 (t80) REVERT: D 233 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8539 (mm-30) outliers start: 30 outliers final: 15 residues processed: 383 average time/residue: 0.4585 time to fit residues: 250.1048 Evaluate side-chains 335 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 318 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072293 restraints weight = 105727.718| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 4.22 r_work: 0.3123 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10700 Z= 0.153 Angle : 0.545 4.228 14452 Z= 0.298 Chirality : 0.035 0.136 1624 Planarity : 0.004 0.057 1756 Dihedral : 4.107 23.733 1408 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.03 % Favored : 94.33 % Rotamer: Outliers : 1.91 % Allowed : 12.76 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1252 helix: 1.71 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.83 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 294 HIS 0.001 0.000 HIS A 30 PHE 0.013 0.001 PHE B 252 TYR 0.012 0.001 TYR C 185 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 760) hydrogen bonds : angle 4.29377 ( 2208) covalent geometry : bond 0.00302 (10700) covalent geometry : angle 0.54471 (14452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 344 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ARG cc_start: 0.8764 (mpt-90) cc_final: 0.8541 (mpt-90) REVERT: A 221 ASP cc_start: 0.8225 (t0) cc_final: 0.7929 (m-30) REVERT: A 233 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8486 (mm-30) REVERT: B 195 ARG cc_start: 0.8751 (mpt-90) cc_final: 0.8519 (mpt-90) REVERT: B 204 TYR cc_start: 0.9125 (t80) cc_final: 0.8883 (t80) REVERT: B 221 ASP cc_start: 0.8225 (t0) cc_final: 0.7933 (m-30) REVERT: B 233 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8508 (mm-30) REVERT: C 221 ASP cc_start: 0.8203 (t0) cc_final: 0.7923 (m-30) REVERT: C 233 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8499 (mm-30) REVERT: C 289 GLU cc_start: 0.8921 (tp30) cc_final: 0.8629 (tp30) REVERT: D 62 CYS cc_start: 0.9449 (p) cc_final: 0.9237 (p) REVERT: D 185 TYR cc_start: 0.9327 (t80) cc_final: 0.9053 (t80) REVERT: D 204 TYR cc_start: 0.9241 (t80) cc_final: 0.8732 (t80) REVERT: D 233 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8526 (mm-30) outliers start: 22 outliers final: 12 residues processed: 345 average time/residue: 0.4914 time to fit residues: 245.0377 Evaluate side-chains 323 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 311 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072449 restraints weight = 108471.023| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.33 r_work: 0.3130 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10700 Z= 0.157 Angle : 0.523 4.396 14452 Z= 0.292 Chirality : 0.034 0.127 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.076 25.461 1408 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.59 % Favored : 93.77 % Rotamer: Outliers : 1.91 % Allowed : 13.89 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1252 helix: 1.91 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 294 HIS 0.001 0.000 HIS C 30 PHE 0.009 0.001 PHE A 202 TYR 0.009 0.001 TYR C 61 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 760) hydrogen bonds : angle 4.18090 ( 2208) covalent geometry : bond 0.00320 (10700) covalent geometry : angle 0.52273 (14452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 326 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.9534 (tp) cc_final: 0.9198 (tp) REVERT: A 185 TYR cc_start: 0.9335 (t80) cc_final: 0.8989 (t80) REVERT: A 204 TYR cc_start: 0.9148 (t80) cc_final: 0.8892 (t80) REVERT: A 233 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 66 ILE cc_start: 0.9555 (tp) cc_final: 0.9224 (tp) REVERT: B 161 MET cc_start: 0.9598 (ttp) cc_final: 0.9322 (ptm) REVERT: B 180 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8623 (tp40) REVERT: B 185 TYR cc_start: 0.9346 (t80) cc_final: 0.9023 (t80) REVERT: B 204 TYR cc_start: 0.9115 (t80) cc_final: 0.8821 (t80) REVERT: B 233 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8662 (mm-30) REVERT: C 127 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 185 TYR cc_start: 0.9379 (t80) cc_final: 0.9112 (t80) REVERT: C 204 TYR cc_start: 0.9186 (t80) cc_final: 0.8922 (t80) REVERT: C 233 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8649 (mm-30) REVERT: C 289 GLU cc_start: 0.8915 (tp30) cc_final: 0.8680 (tp30) REVERT: D 127 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7341 (t80) REVERT: D 204 TYR cc_start: 0.9253 (t80) cc_final: 0.8641 (t80) REVERT: D 233 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8644 (mm-30) outliers start: 22 outliers final: 11 residues processed: 332 average time/residue: 0.4666 time to fit residues: 221.9297 Evaluate side-chains 301 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.081391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069193 restraints weight = 111711.487| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.18 r_work: 0.3074 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10700 Z= 0.258 Angle : 0.584 5.214 14452 Z= 0.332 Chirality : 0.037 0.146 1624 Planarity : 0.004 0.052 1756 Dihedral : 4.216 28.190 1408 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.23 % Favored : 93.21 % Rotamer: Outliers : 1.91 % Allowed : 15.97 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1252 helix: 1.89 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.25 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 294 HIS 0.002 0.001 HIS A 30 PHE 0.013 0.001 PHE D 211 TYR 0.013 0.002 TYR D 61 ARG 0.004 0.001 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 760) hydrogen bonds : angle 4.39281 ( 2208) covalent geometry : bond 0.00521 (10700) covalent geometry : angle 0.58352 (14452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8984 (tp40) cc_final: 0.8671 (tp40) REVERT: A 181 GLN cc_start: 0.8517 (pm20) cc_final: 0.8268 (pm20) REVERT: A 185 TYR cc_start: 0.9318 (t80) cc_final: 0.9097 (t80) REVERT: A 289 GLU cc_start: 0.9014 (tp30) cc_final: 0.8790 (tp30) REVERT: B 127 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7436 (t80) REVERT: B 185 TYR cc_start: 0.9371 (t80) cc_final: 0.9111 (t80) REVERT: B 289 GLU cc_start: 0.9016 (tp30) cc_final: 0.8799 (tp30) REVERT: C 127 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7516 (t80) REVERT: C 279 MET cc_start: 0.9268 (mtp) cc_final: 0.9067 (mtp) REVERT: C 289 GLU cc_start: 0.8957 (tp30) cc_final: 0.8596 (tp30) REVERT: D 127 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7488 (t80) outliers start: 22 outliers final: 18 residues processed: 316 average time/residue: 0.4367 time to fit residues: 200.1102 Evaluate side-chains 302 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068956 restraints weight = 111166.377| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.22 r_work: 0.3069 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10700 Z= 0.225 Angle : 0.549 4.683 14452 Z= 0.308 Chirality : 0.036 0.148 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.229 28.017 1408 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.87 % Favored : 92.65 % Rotamer: Outliers : 2.69 % Allowed : 17.62 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1252 helix: 1.94 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.001 0.000 HIS B 30 PHE 0.011 0.001 PHE A 211 TYR 0.012 0.001 TYR D 61 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 760) hydrogen bonds : angle 4.29249 ( 2208) covalent geometry : bond 0.00455 (10700) covalent geometry : angle 0.54920 (14452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8748 (tp40) cc_final: 0.8152 (tp40) REVERT: A 233 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8640 (mm-30) REVERT: A 289 GLU cc_start: 0.8959 (tp30) cc_final: 0.8646 (tp30) REVERT: B 127 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 185 TYR cc_start: 0.9313 (t80) cc_final: 0.9001 (t80) REVERT: B 233 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8659 (mm-30) REVERT: B 289 GLU cc_start: 0.9002 (tp30) cc_final: 0.8707 (tp30) REVERT: C 114 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8795 (tm-30) REVERT: C 161 MET cc_start: 0.9567 (ttp) cc_final: 0.9366 (ptm) REVERT: C 190 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8625 (tp30) REVERT: C 195 ARG cc_start: 0.8768 (mpt-90) cc_final: 0.8566 (mpt-90) REVERT: C 233 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8661 (mm-30) REVERT: C 289 GLU cc_start: 0.8966 (tp30) cc_final: 0.8586 (tp30) REVERT: D 185 TYR cc_start: 0.9404 (t80) cc_final: 0.9149 (t80) REVERT: D 195 ARG cc_start: 0.8715 (mpt-90) cc_final: 0.8499 (mpt-90) REVERT: D 233 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8723 (mm-30) REVERT: D 289 GLU cc_start: 0.8978 (tp30) cc_final: 0.8655 (tp30) outliers start: 31 outliers final: 20 residues processed: 301 average time/residue: 0.4511 time to fit residues: 195.8374 Evaluate side-chains 311 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.070758 restraints weight = 108647.692| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.22 r_work: 0.3104 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10700 Z= 0.133 Angle : 0.528 5.724 14452 Z= 0.285 Chirality : 0.036 0.164 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.105 26.091 1408 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.39 % Favored : 93.13 % Rotamer: Outliers : 3.21 % Allowed : 17.80 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1252 helix: 2.17 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.000 0.000 HIS A 30 PHE 0.007 0.001 PHE B 127 TYR 0.010 0.001 TYR B 185 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 760) hydrogen bonds : angle 3.95657 ( 2208) covalent geometry : bond 0.00282 (10700) covalent geometry : angle 0.52801 (14452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.9263 (tt0) cc_final: 0.8977 (tt0) REVERT: A 180 GLN cc_start: 0.8485 (tp40) cc_final: 0.8251 (tp40) REVERT: A 204 TYR cc_start: 0.9211 (t80) cc_final: 0.8741 (t80) REVERT: A 233 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8647 (mm-30) REVERT: B 127 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 195 ARG cc_start: 0.8734 (mpt-90) cc_final: 0.8534 (mpt-90) REVERT: B 204 TYR cc_start: 0.9193 (t80) cc_final: 0.8799 (t80) REVERT: B 233 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8692 (mm-30) REVERT: C 161 MET cc_start: 0.9532 (ttp) cc_final: 0.9312 (ptm) REVERT: C 180 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8792 (tp40) REVERT: C 204 TYR cc_start: 0.9205 (t80) cc_final: 0.8770 (t80) REVERT: C 233 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8652 (mm-30) REVERT: D 190 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: D 233 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8754 (mm-30) outliers start: 37 outliers final: 22 residues processed: 314 average time/residue: 0.4731 time to fit residues: 217.9684 Evaluate side-chains 312 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 281 GLU Chi-restraints excluded: chain D residue 301 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0111 > 50: distance: 129 - 168: 3.260 distance: 133 - 187: 14.673 distance: 144 - 208: 30.898 distance: 157 - 228: 4.523 distance: 170 - 187: 13.341 distance: 187 - 188: 21.360 distance: 187 - 199: 11.354 distance: 188 - 189: 6.172 distance: 188 - 191: 14.695 distance: 188 - 200: 31.197 distance: 189 - 190: 16.068 distance: 189 - 208: 58.132 distance: 191 - 192: 3.470 distance: 191 - 201: 10.649 distance: 191 - 202: 13.967 distance: 192 - 193: 9.380 distance: 192 - 194: 5.149 distance: 193 - 195: 8.627 distance: 193 - 203: 4.242 distance: 194 - 196: 5.242 distance: 194 - 204: 3.849 distance: 195 - 197: 3.367 distance: 195 - 205: 3.788 distance: 196 - 197: 5.445 distance: 196 - 206: 5.472 distance: 197 - 198: 5.460 distance: 198 - 207: 10.276 distance: 208 - 209: 37.183 distance: 208 - 219: 38.886 distance: 209 - 210: 19.112 distance: 209 - 212: 33.978 distance: 209 - 220: 25.233 distance: 210 - 211: 17.130 distance: 210 - 228: 11.075 distance: 212 - 213: 13.724 distance: 212 - 221: 6.499 distance: 212 - 222: 11.473 distance: 213 - 214: 9.503 distance: 213 - 215: 3.429 distance: 214 - 216: 6.616 distance: 214 - 223: 9.279 distance: 215 - 217: 4.386 distance: 215 - 224: 4.363 distance: 216 - 218: 3.219 distance: 216 - 225: 5.178 distance: 217 - 218: 6.785 distance: 217 - 226: 3.962 distance: 228 - 229: 5.217 distance: 228 - 234: 7.731 distance: 229 - 230: 10.971 distance: 229 - 232: 6.097 distance: 229 - 235: 7.840 distance: 230 - 231: 15.358 distance: 230 - 239: 7.427 distance: 232 - 233: 15.392 distance: 232 - 236: 10.735 distance: 232 - 237: 17.234 distance: 233 - 238: 11.545 distance: 239 - 240: 8.845 distance: 239 - 248: 6.742 distance: 240 - 241: 5.766 distance: 240 - 243: 8.531 distance: 240 - 249: 14.501 distance: 241 - 242: 11.446 distance: 241 - 256: 8.766 distance: 243 - 244: 4.274 distance: 243 - 250: 4.167 distance: 243 - 251: 7.016 distance: 244 - 245: 7.391 distance: 244 - 252: 9.628 distance: 244 - 253: 12.490 distance: 245 - 246: 8.944 distance: 245 - 247: 6.210 distance: 247 - 254: 9.569 distance: 247 - 255: 8.997 distance: 256 - 257: 9.013 distance: 256 - 267: 12.704 distance: 257 - 258: 12.502 distance: 257 - 260: 6.501 distance: 257 - 268: 14.040 distance: 258 - 259: 12.452 distance: 258 - 280: 13.212 distance: 260 - 261: 12.676 distance: 260 - 269: 18.356 distance: 260 - 270: 14.037 distance: 261 - 262: 15.474 distance: 261 - 271: 18.032 distance: 261 - 272: 19.108 distance: 262 - 263: 8.233 distance: 262 - 273: 15.832 distance: 262 - 274: 12.859 distance: 263 - 264: 3.098 distance: 263 - 275: 10.656 distance: 264 - 266: 4.355 distance: 265 - 276: 5.658 distance: 265 - 277: 5.982 distance: 266 - 278: 4.042 distance: 280 - 281: 5.306 distance: 280 - 289: 15.900 distance: 281 - 282: 8.361 distance: 281 - 284: 11.789 distance: 281 - 290: 12.998 distance: 282 - 283: 22.546 distance: 282 - 302: 14.496 distance: 284 - 285: 5.668 distance: 284 - 291: 9.957 distance: 284 - 292: 11.851 distance: 285 - 286: 13.382 distance: 285 - 293: 6.424 distance: 285 - 294: 7.947 distance: 286 - 287: 6.751 distance: 286 - 295: 4.100 distance: 286 - 296: 5.677 distance: 287 - 288: 8.372 distance: 287 - 297: 6.663 distance: 287 - 298: 12.338 distance: 288 - 299: 3.706 distance: 302 - 303: 11.345 distance: 302 - 311: 24.936 distance: 303 - 304: 17.955 distance: 303 - 306: 16.032 distance: 303 - 312: 31.833 distance: 304 - 305: 24.297 distance: 304 - 317: 23.765 distance: 305 - 364: 24.851 distance: 306 - 307: 8.646 distance: 306 - 313: 22.800 distance: 306 - 314: 22.258 distance: 307 - 308: 15.386 distance: 307 - 315: 12.728 distance: 307 - 316: 18.151 distance: 308 - 309: 16.965 distance: 308 - 310: 12.339 distance: 317 - 318: 14.234 distance: 317 - 329: 14.452 distance: 318 - 319: 11.089 distance: 318 - 321: 16.808 distance: 318 - 330: 18.895 distance: 319 - 320: 5.253 distance: 319 - 338: 7.700 distance: 320 - 375: 16.326 distance: 321 - 322: 7.409 distance: 321 - 331: 24.312 distance: 321 - 332: 18.530 distance: 322 - 324: 12.250 distance: 323 - 325: 5.944 distance: 323 - 333: 3.859 distance: 324 - 326: 14.860 distance: 324 - 334: 11.487 distance: 325 - 327: 6.503 distance: 325 - 335: 21.100 distance: 326 - 327: 13.373 distance: 326 - 336: 10.227 distance: 327 - 328: 10.092 distance: 328 - 337: 9.063 distance: 338 - 339: 4.016 distance: 338 - 345: 16.897 distance: 339 - 340: 7.860 distance: 339 - 342: 7.890 distance: 339 - 346: 8.585 distance: 340 - 341: 8.712 distance: 340 - 354: 10.417 distance: 341 - 388: 6.389 distance: 342 - 343: 12.690 distance: 342 - 347: 5.931 distance: 343 - 348: 9.137 distance: 343 - 349: 6.152 distance: 343 - 350: 15.251 distance: 344 - 351: 11.130 distance: 344 - 352: 6.194 distance: 344 - 353: 3.976 distance: 354 - 355: 6.270 distance: 354 - 359: 7.317 distance: 355 - 356: 4.667 distance: 355 - 358: 3.110 distance: 355 - 360: 4.820 distance: 356 - 357: 9.057 distance: 356 - 364: 4.808 distance: 357 - 402: 7.874 distance: 358 - 361: 4.579 distance: 358 - 362: 21.311 distance: 358 - 363: 6.039